EP2202320A1 - Methods and means for typing a sample comprising colorectal cancer cells - Google Patents

Methods and means for typing a sample comprising colorectal cancer cells Download PDF

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EP2202320A1
EP2202320A1 EP08172911A EP08172911A EP2202320A1 EP 2202320 A1 EP2202320 A1 EP 2202320A1 EP 08172911 A EP08172911 A EP 08172911A EP 08172911 A EP08172911 A EP 08172911A EP 2202320 A1 EP2202320 A1 EP 2202320A1
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genes
rna
colorectal cancer
individual
sample
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French (fr)
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Agendia NV
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Priority to EP08172911A priority Critical patent/EP2202320A1/en
Priority to EP09775361A priority patent/EP2379740A1/en
Priority to NZ593847A priority patent/NZ593847A/en
Priority to AU2009330807A priority patent/AU2009330807B2/en
Priority to MX2011006926A priority patent/MX2011006926A/en
Priority to PCT/NL2009/050797 priority patent/WO2010074573A1/en
Priority to CN200980157369.0A priority patent/CN102325902B/en
Priority to JP2011543452A priority patent/JP2012513752A/en
Priority to US13/141,742 priority patent/US8921051B2/en
Priority to CA2748224A priority patent/CA2748224A1/en
Publication of EP2202320A1 publication Critical patent/EP2202320A1/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the invention relates to the field of oncology. More specifically, the invention relates to a method for typing colorectal cancer cells.
  • the invention provides means and methods for differentiating colorectal cancer cells with a low metastasizing potential and with a high metastatic potential.
  • Colorectal cancer is the third most common cancer worldwide after lung and breast with two-thirds of all colorectal cancers occurring in the more developed regions. As with all cancers, chances of survival are good for patients when the cancer is detected in an early stage. Stage I patients have a survival rate of ⁇ 93% while the 5-year survival rate drops to ⁇ 80% in stage II patients and to 60% in stage III patients ( Sobrero et al., 2006. The Lancet Oncology 7(6): 515-517 ).
  • stage III For stage III patients, adjuvant treatment is recommended for all patients ( Gill et al., 2004. Journal of Clinical Oncology 22: 1797-1806 ) although patients with T1 or T2 N1 MO tumors (stage IIIA) have a significantly better survival rate than stage II B patients indicating that many patients would not require additional chemotherapy.
  • the invention provides a method for typing a RNA sample of an individual suffering from colorectal cancer or suspected of suffering there from, the method comprising providing an RNA sample that is prepared from a tissue sample from said individual, said tissue sample comprising colorectal cancer cells or suspected to comprise colorectal cancer cells; determining RNA levels for a set of genes in said RNA sample; and typing said RNA sample on the basis of the RNA levels determined for said set of genes; wherein said set of genes comprises at least two of the genes listed in Table 1.
  • This study discloses a robust gene expression signature that predicts disease relapse and be added to current clinicopathological risk assessment to assist physicians in making treatment decisions.
  • the identification of the sub-group of patients that are more likely to suffer from a recurrent disease allows the identification of patients who are more likely to benefit from adjuvant chemotherapy and should be treated after surgery.
  • the present gene expression signature was identified after removing to a large extent training samples comprising cancer cells with an activating mutation in B-Raf (BRAF mut ).
  • BRAF mut colon cancer samples were found to be highly variable in gene expression data which masked more general, prognosis-related gene expression data. Without being bound by theory, said variable gene expression might be caused by a high degree of micro-satellite instability (MSI) in BRAF mut colon cancer samples.
  • MSI micro-satellite instability
  • Colorectal cancer is a type of cancer that originates in the large intestine or bowel, comprising the colon and the rectum. Colon cancer and rectal cancer have many features in common. The majority of colorectal cancers are adenocarcinomas. These are cancers of the cells that line the inside layer of the wall of the colon and rectum.
  • tumors may also develop in the colon and rectum, such as carcinoid tumors, which develop from specialized hormone-producing cells of the intestine; gastrointestinal stromal tumors or leiomyosarcomas, which develop from smooth muscle cells in the wall of the intestine; and lymphomas, which are cancers of immune system cells that typically develop in lymph nodes but also may start in the colon and rectum or other organs.
  • carcinoid tumors which develop from specialized hormone-producing cells of the intestine
  • gastrointestinal stromal tumors or leiomyosarcomas which develop from smooth muscle cells in the wall of the intestine
  • lymphomas which are cancers of immune system cells that typically develop in lymph nodes but also may start in the colon and rectum or other organs.
  • Adenocarcinomas usually start as a colorectal polyp, a hyperplasia which is defined as a visible protrusion above the surface of the surrounding normal large bowel mucosa.
  • Colorectal polyps are classified as either neoplastic (adenomatous polyps) or non-neoplastic, comprising hyperplastic, mucosal, inflammatory, and hamartomatous polyps which have no malignant potential.
  • Adenomatous polyps, or adenomas are attached to the bowel wall by a stalk (pedunculated) or by a broad, flat base (sessile).
  • a colorectal hyperplasia or polyp can develop into a malignant adenocarcinoma.
  • RNA isolated from a training set of colorectal samples with a wild type B-Raf gene and comprising samples from colorectal cancers that did not give rise to metastases in patients within the length of follow up time of each patient; and samples from colorectal cancers that gave rise to metastases in patients within the length of follow up time of each patient genes were selected using a multivariate Cox Regression based method ( Simon et al., Design and Analysis of DNA Microarray Investigations, Springer-Verlag New York, (2003 ); Korn et al.,. Journal of Statistical Planning and Inference 124, 379-398 (2004 )).
  • RNA levels were significantly related to survival of the patient, independent of patient stage, where survival is defined as being free of cancer recurrence.
  • survival is defined as being free of cancer recurrence.
  • Each of the genes listed in Table 1 was shown to be predictive of survival and have a minimum significance threshold of 0.001.
  • a set of at least two genes comprises MCTP1 (SEQ ID NO 36) and THNSL2 (SEQ ID NO 13). More preferred is the determination of a ratio of expression of MCTP1 (SEQ ID NO 36) and THNSL2 (SEQ ID NO 13).
  • a sample with a determined MCTP1/THNSLC2 ratio above a predetermined threshold is indicative of a sample with a low risk of cancer recurrence.
  • Samples with a high MCTP1/THNSLC2 ratio showed a 5-year distant metastasis free survival (DMSF) of 87%.
  • Samples with a low MCTP1/THNSLC2 ratio (high-risk) showed a DMFS of 70%.
  • a set of genes according to the invention comprises at least three of the genes listed in Table 1, more preferred at least four of the genes listed in Table 1, more preferred at least five of the genes listed in Table 1, more preferred at least six of the genes listed in Table 1, more preferred at least seven of the genes listed in Table 1, more preferred at least eight of the genes listed in Table 1, more preferred at least nine of the genes listed in Table 1, more preferred at least ten of the genes listed in Table 1, more preferred at least fifteen of the genes listed in Table 1, more preferred at least twenty of the genes listed in Table 1, more preferred at least twenty-five of the genes listed in Table 1, more preferred at least thirty of the genes listed in Table 1, more preferred at least forty of the genes listed in Table 1, more preferred at least fifty of the genes listed in Table 1, more preferred at least sixty of the genes listed in Table 1, more preferred at least seventy of the genes listed in Table 1, more preferred at least eighty of the genes listed in Table 1, more preferred hundred of the genes listed in Table 1, more preferred hundred-fifty of the genes listed in Table 1, more preferred two-hundred of
  • a preferred set of genes for use in a method of the invention comprises the first two rank-ordered genes listed in Table 1, more preferred the first three rank-ordered genes, more preferred the first four rank-ordered genes, more preferred the first five rank-ordered genes, more preferred the first six rank-ordered genes, more preferred the first seven rank-ordered genes, more preferred the first eight rank-ordered genes, more preferred the first ten rank-ordered genes, more preferred the first fifteen rank-ordered genes, more preferred the first twenty rank-ordered genes, more preferred the first thirty rank-ordered genes, more preferred the first fourty rank-ordered genes, more preferred the first fifty rank-ordered genes, more preferred the first sixty rank-ordered genes, more preferred the first seventy rank-ordered genes, more preferred the first eighty rank-ordered genes, more preferred the first ninety rank-ordered genes, more preferred the first hundred rank-ordered genes, more preferred the first hundred-fifty rank-ordered genes
  • a preferred signature comprises genes referred to in Table 1 as ZBED4, LIF, PIM3, IL2RA, PYROXD1, CTSC, EDEM1, M6PRBP1, SLC6A12, THNSL2, PPARA, ZNF697, LAMA3, CA438802, MCTP1, HSD3B1, CYFIP2, IL2RB.
  • a further preferred signature comprises genes referred to in Table 1 as ZBED4, LIF, IL18R1, PIM3, IL2RA, PYROXD1, CTSC, EDEM1, M6PRBP1, SLC6A12, THNSL2, KCNJ10, THC2663361, C10orf67, KIAA0040, BC040628, AK096685, PIGW, PPARA, COLQ, AK021427, C15orf27, PRDM4, LOC165186, ZNF697, CRYGA, EEPD1, LAMA3, NEDD8, CA438802, MCTP1, HSD3B1, CYFIP2, IL2RB, XKR3, NT_035113, THC2520461, and THC2662025.
  • Table 1 ZBED4, LIF, IL18R1, PIM3, IL2RA, PYROXD1, CTSC, EDEM1, M6PRBP1, SLC6A12, THNSL2, KCNJ10
  • a cell sample is a clinically relevant sample that comprises a colorectal cancer cell or an expression product comprising a nucleic acid from a colorectal cancer cell.
  • a cell sample according to the invention is obtained directly from the large intestine during surgery.
  • the cell sample is prepared from a biopsy sample that is taken during colonoscopy.
  • the biopsies have a depth of at most 10 millimeter, more preferred at most 5 millimeter, with a preferred diameter of about 2 millimeter, more preferred about 3 millimeter, more preferred about 4 millimeter, more preferred about 5 millimeter, more preferred about 6 millimeter, more preferred about 7 millimeter, more preferred about 8 millimeter, more preferred about 9 millimeter, more preferred about 10 millimeter.
  • a preferred diameter of about 2 millimeter more preferred about 3 millimeter, more preferred about 4 millimeter, more preferred about 5 millimeter, more preferred about 6 millimeter, more preferred about 7 millimeter, more preferred about 8 millimeter, more preferred about 9 millimeter, more preferred about 10 millimeter.
  • other forms that are equal in size and total volume are also possible.
  • the tissue sample comprises stool or blood voided by a patient suffering from colorectal cancer, said tissue sample comprising a colorectal cancer cell or a gene expression product such as a nucleic acid product from a colorectal cancer cell.
  • Methods to purify cells or gene expression products such as RNA from human stool or blood samples are known in the art and have been described for example in patent application W0199820355 , W02003068788 , and Yang et al. 2005. Cancer Lett 226: 55-63 , which are enclosed by reference.
  • Samples can be processed in numerous ways, as is known to a skilled person. For example, they can be freshly prepared from cells or tissues at the moment of harvesting, or they can be prepared from samples that are stored at -70°C until processed for sample preparation. Alternatively, tissues, biopsies, stool or blood samples can be stored under conditions that preserve the quality of the protein or RNA. Examples of these preservative conditions are fixation using e.g.
  • RNAsin RNAsin
  • RNasecure aquous solutions
  • aquous solutions such as RNAlater (Assuragen; US06204375 ), Hepes-Glutamic acid buffer mediated Organic solvent Protection Effect (HOPE; DE10021390 ), and RCL2 (Alphelys; W004083369 )
  • non-aquous solutions such as Universal Molecular Fixative (Sakura Finetek USA Inc.; US7138226 ).
  • RNA level of at least two of the genes listed in Table 1 can be determined by any method known in the art. Methods to determine RNA levels of genes are known to a skilled person and include, but are not limited to, Northern blotting, quantitative PCR, and microarray analysis.
  • Northern blotting comprises the quantification of the nucleic acid expression product of a specific gene by hybridizing a labeled probe that specifically interacts with said nucleic acid expression product, after separation of nucleic acid expression products by gel electrophoreses. Quantification of the labeled probe that has interacted with said nucleic acid expression product serves as a measure for determining the level of expression.
  • the determined level of expression can be normalized for differences in the total amounts of nucleic acid expression products between two separate samples by comparing the level of expression of a gene that is known not to differ in expression level between samples.
  • Quantitative Polymerase Chain Reaction provides an alternative method to quantify the level of expression of nucleic acids.
  • qPCR can be performed by real-time PCR (rtPCR), in which the amount of product is monitored during the reaction, or by end-point measurements, in which the amount of a final product is determined.
  • rtPCR can be performed by either the use of a nucleic acid intercalator, such as for example ethidium bromide or SYBR® Green I dye, which interacts which all generated double stranded products resulting in an increase in fluorescence during amplification, or by the use of labeled probes that react specifically with the generated double stranded product of the gene of interest.
  • Alternative detection methods that can be used are provided by dendrimer signal amplification, hybridization signal amplification, and molecular beacons.
  • amplification methods known to a skilled artisan, can be employed for qPCR, including but not limited to PCR, rolling circle amplification, nucleic acid sequence-based amplification, transcription mediated amplification, and linear RNA amplification.
  • qPCR methods such as reverse transcriptase- multiplex ligation-dependent amplification (rtMLPA), which accurately quantifies up to 45 transcripts of interest in a one-tube assay ( Eldering et al., Nucleic Acids Res 2003; 31: e153 ) can be employed.
  • rtMLPA reverse transcriptase- multiplex ligation-dependent amplification
  • a microarray usually comprises nucleic acid molecules, termed probes, which are able to hybridize to nucleic acid expression products.
  • the probes are exposed to labeled sample nucleic acid, hybridized, and the abundance of nucleic acid expression products in the sample that are complementary to a probe is determined.
  • the probes on a microarray may comprise DNA sequences, RNA sequences, or copolymer sequences of DNA and RNA.
  • the probes may also comprise DNA and/or RNA analogues such as, for example, nucleotide analogues or peptide nucleic acid molecules (PNA), or combinations thereof.
  • the sequences of the probes may be full or partial fragments of genomic DNA.
  • the sequences may also be in vitro synthesized nucleotide sequences, such as synthetic oligonucleotide sequences.
  • RNA levels are determined simultaneously.
  • Simultaneous analyses can be performed, for example, by multiplex qPCR and microarray analysis.
  • Microarray analyses allow the simultaneous determination of the nucleic acid levels of expression of a large number of genes, such as more than 50 genes, more than 100 genes, more than 1000 genes, or even more than 10.000 genes, allowing the use of a large number of gene expression data for normalization of the genes comprising the colorectal expression profile.
  • RNA levels are determined by microarray analysis.
  • a probe is specific for a gene listed in Table 1.
  • a probe can be specific when it comprises a continuous stretch of nucleotides that are completely complementary to a nucleotide sequence of a RNA product of said gene, or a cDNA product thereof.
  • a probe can also be specific when it comprises a continuous stretch of nucleotides that are partially complementary to a nucleotide sequence of a RNA product of said gene, or a cDNA product thereof. Partially means that a maximum of 5% from the nucleotides in a continuous stretch of at least 20 nucleotides differs from the corresponding nucleotide sequence of a RNA product of said gene.
  • the term complementary is known in the art and refers to a sequence that is related by base-pairing rules to the sequence that is to be detected. It is preferred that the sequence of the probe is carefully designed to minimize nonspecific hybridization to said probe. It is preferred that the probe is or mimics a single stranded nucleic acid molecule.
  • the length of said complementary continuous stretch of nucleotides can vary between 15 bases and several kilo bases, and is preferably between 20 bases and 1 kilobase, more preferred between 40 and 100 bases, and most preferred 60 nucleotides.
  • a most preferred probe comprises a continuous stretch of 60 nucleotides that are identical to a nucleotide sequence of a RNA product of a gene, or a cDNA product thereof.
  • the RNA sample is preferably labeled, either directly or indirectly, and contacted with probes on the array under conditions that favor duplex formation between a probe and a complementary molecule in the labeled RNA sample.
  • the amount of label that remains associated with a probe after washing of the microarray can be determined and is used as a measure for the level of RNA of a nucleic acid molecule that is complementary to said probe.
  • the determined RNA levels for at least two genes listed in Table 1 can be normalized to correct for systemic bias.
  • Systemic bias results in variation by inter-array differences in overall performance, which can be due to for example inconsistencies in array fabrication, staining and scanning, and variation between labeled RNA samples, which can be due for example to variations in purity.
  • Systemic bias can be introduced during the handling of the sample in a microarray experiment.
  • the determined RNA levels are preferably corrected for background non-specific hybridization and normalized using, for example, Feature Extraction software (Agilent Technologies).
  • the array may comprise specific probes that are used for normalization. These probes preferably detect RNA products from housekeeping genes such as glyceraldehyde-3-phosphate dehydrogenase and 18S rRNA levels, of which the RNA level is thought to be constant in a given cell and independent from the developmental stage or prognosis of said cell.
  • a preferred method according to the invention further comprises normalizing the determined RNA levels of said set of at least two of the genes listed in Table 1 in said sample.
  • Said normalization preferably comprises median centering, in which the "centers" of the array data are brought to the same level under the assumption that the majority of genes are un-changed between conditions.
  • Said normalization preferably comprises Lowess (LOcally WEighted Scatterplot Smoothing) local regression normalization to correct for both print-tip and intensity-dependent bias.
  • genes are selected of which the RNA levels are largely constant between different tissue samples comprising colorectal cells from one individual, and between tissue samples comprising colorectal cells from different individuals. It is furthermore preferred that RNA levels of said set of normalization genes differ between the genes. For example, it is preferred to select genes with a low RNA level in said tissue sample, and genes with a high RNA level. More preferred is to select genes with a low RNA level in said tissue sample, genes with a moderate RNA level, and genes with a high RNA level. It will be clear to a skilled artisan that the RNA levels of said set of normalization genes preferably allow normalization over the whole range of RNA levels.
  • a preferred method further comprises multiplying each of the normalized expression values with a predetermined constant for said gene to obtain a weighted value for the relative RNA level of said gene, and thereby a set of weighted values for said set of genes, said method further comprising typing said sample on the basis of said set of weighted values.
  • Said set of weighted values can be summed and compared to a summed set of weighted values from a reference sample. It is preferred that said summed set of weighted values is compared to a classification threshold, that is determined by the values obtained from RNA samples of which the typing is known.
  • a staging system is provided by the TNM Staging System, which combines data about the Tumor (T), the spread to lymph nodes (N), and the existence of distant metastases (M).
  • TNM stage I colorectal cancer is defined as a cancer that began to spread and has invaded the submucosa or the muscularis propria.
  • TNM stage II defines a cancer that has invaded through the muscularis basement into the subserosa, or into the horric or perirectal tissues, but has not reached the lymph nodes.
  • a stage III defines a cancer that has spread to the lymph nodes in the absence of distant metastases.
  • a stage IV defines a cancer that has spread to distant sites.
  • the invention provides a method of typing an individual suffering from colorectal cancer, wherein said colorectal cancer comprises a TNM stage I, TNM stage II or TNM stage III colorectal cancer as determined by the TNM Staging System, wherein TNM stage II and TNM stage III are preferred colorectal cancers.
  • said typing in a method according to the invention allows differentiating cancer cells with a low metastasizing potential or risk of cancer recurrence and cancer cells with a high metastatic potential or risk of cancer recurrence.
  • RNA levels at least two of the genes listed in Table 1 can be compared to RNA levels of said genes in a reference sample.
  • a reference sample is preferably an RNA sample isolated from a colorectal tissue from a healthy individual, or an RNA sample from a relevant cell line or mixture of cell lines.
  • Said reference sample can also be an RNA sample from a cancerous growth of an individual suffering from colorectal cancer.
  • Said individual suffering from colorectal cancer can have an increased risk of cancer recurrence, or a low risk of cancer recurrence.
  • said reference sample is an RNA sample from an individual suffering from colorectal cancer and having a low risk of cancer recurrence.
  • said reference sample is a pooled RNA sample from multiple tissue samples comprising colorectal cells from individuals suffering from colorectal cancer and having a low risk of cancer recurrence. It is preferred that said multiple tissue sample comprises more than 10 tissue samples, more preferred more than 20 tissue samples, more preferred more than 30 tissue samples, more preferred more than 40 tissue samples, most preferred more than 50 tissue samples.
  • a most preferred reference sample comprises pooled RNA from multiple tissue samples comprising colorectal cancer cells from individuals having a low risk of cancer recurrence and from individuals having a high risk of cancer recurrence.
  • a further preferred reference sample comprises RNA isolated and pooled from colon tissue from healthy individuals, or from so called normal adjacent tissue from colon cancer patients or RNA from a generic cell line or cell line mixture.
  • the RNA from a cell line or cell line mixture can be produced in-house or obtained from a commercial source such as, for example, Stratagene Human Reference RNA.
  • a coefficient is determined that is a measure of a similarity or dissimilarity of a sample with said reference sample.
  • a number of different coefficients can be used for determining a correlation between the RNA expression level in an RNA sample from an individual and a reference sample.
  • Preferred methods are parametric methods which assume a normal distribution of the data. One of these methods is the Pearson product-moment correlation coefficient, which is obtained by dividing the covariance of the two variables by the product of their standard deviations.
  • Preferred methods comprise cosine-angle, un-centered correlation and, more preferred, cosine correlation ( Fan et al., Conf Proc IEEE Eng Med Biol Soc. 5:4810-3 (2005 )).
  • said correlation with a reference sample is used to produce an overall similarity score for the set of genes that are used.
  • a similarity score is a measure of the average correlation of RNA levels of a set of genes in an RNA sample from an individual and a reference sample.
  • Said similarity score can, for example, be a numerical value between +1, indicative of a high correlation between the RNA expression level of the set of genes in a RNA sample of said individual and said reference sample, and -1, which is indicative of an inverse correlation and therefore indicative of having an increased risk of cancer recurrence ( van 't Veer et al., Nature 415: 484-5 (2002 )).
  • the invention provides a method of classifying an individual suffering from colorectal cancer, comprising classifying said individual as having a poor prognosis or a good prognosis by a method comprising determining a similarity value between RNA levels from a set of at least two genes listed in Table 1 in a RNA sample from said individual and a level of expression from said set of genes in a RNA sample from a patient having no recurrent disease within five years of initial diagnosis, and classifying said individual as having a poor prognosis if said similarity value is below a similarity threshold value, and classifying said individual as having a good prognosis if said similarity value exceeds a similarity threshold value.
  • the present invention provides a set of markers useful for distinguishing samples from colorectal cancer patients with a good prognosis from samples from colorectal cancer patients with a poor prognosis.
  • the expression level of these markers is used to determine whether an individual afflicted with colon cancer will have a good or poor clinical prognosis.
  • the invention provides for a method of determining whether an individual afflicted with colon cancer will likely experience a relapse within five years of initial diagnosis (i.
  • Poor prognosis of colon cancer may indicate that a tumor is relatively aggressive, while good prognosis may indicate that a tumor is relatively non-aggressive.
  • the invention provides for a method of determining a course of treatment of a colon cancer patient, comprising determining whether the level of expression of at least two genes of table 1 correlates with the level of these genes in a sample representing a good prognosis expression pattern or a poor prognosis pattern; and determining a course of treatment, wherein if the expression correlates with the poor prognosis pattern, the tumor is treated as an aggressive tumor.
  • a preferred method of classifying a sample as either high or low risk for disease recurrence involves the use of a classification template, derived from Support Vector Machine (SVM) training using all genes identified as being correlated with disease progression.
  • SVM Support Vector Machine
  • Each gene in the template has a corresponding weighing factor, as determined by the SVM implementation by Chang & Lin (Chih-Chung Chang and Chih-Jen Lin, LIBSVM: a library for support vector machines, 2001. http://www.csie.ntu.edu.tw/ ⁇ cjlin/libsvm).
  • This algorithm analyses the information contained in the signature genes across all training set samples and constructs a classification template that best separates patients with recurrence from those without.
  • LIBSVM developed by Chih-Chung Chang and Chih-Jen Lin, is an integrated software for analyzing many problems in supervised classification or regression frameworks.
  • a similarity threshold value is an arbitrary value that allows discriminating between RNA samples from patients with a high risk of cancer recurrence, and RNA samples from patients with a low risk of cancer recurrence.
  • Said similarity threshold value is set at a value at which an acceptable number of patients with known metastasis formation within five years after initial diagnosis would score as false negatives above the threshold value, and an acceptable number of patients without known metastasis formation within five years after initial diagnosis would score as false positives below the threshold value.
  • a similarity score is preferably displayed or outputted to a user interface device, a computer readable storage medium, or a local or remote computer system.
  • the invention provides a method of classifying an individual suffering from colorectal cancer, comprising classifying said individual as having a poor prognosis or a good prognosis by a method comprising (a) providing an RNA sample from a said individual that is prepared from a tissue sample from said individual, said tissue sample comprising colorectal cancer cells or suspected to comprise colorectal cancer cells; (b) determining a level of RNA for a set of genes comprising at least two of the genes listed in Table 1 in said sample; (c) determining a similarity value between a level of expression from the set of genes in said individual and a level of expression from said set of genes in a patient having no recurrent disease within five years of initial diagnosis; and (d) classifying said individual as having a poor prognosis if said similarity value is below a first similarity threshold value, and classifying said individual as having a good prognosis if said similarity value exceeds said first similarity threshold value.
  • the level of RNA for a set of genes comprising at least two of the genes listed in Table 1 in said sample is normalized. Normalization can be performed by any method known to a skilled artisan, including global analysis and the use of specific probes.
  • the invention provides a method of assigning treatment to an individual suffering from colorectal cancer, comprising classifying said individual as having a poor prognosis or a good prognosis according to a method of the invention, and assigning adjuvant chemotherapy if said individual is classified as having poor prognosis.
  • a routine treatment for colorectal cancer is surgery, which is followed by additional treatment if said individual is classified as having poor prognosis.
  • Said additional treatment is selected from adjuvant chemotherapy and radiotherapy.
  • Chemotherapy comprises the use of natural or non-natural compounds to eliminate fast-dividing, and therefore susceptible, cancer cells.
  • Chemotherapeutic compounds comprise alkylating agents such as decarbazine and cyclophosphamide; DNA crosslinking agents such as cisplatin and carboplatin; antimetabolitic agents such as methotrexate, 5-fluorouracil (5FU), and mercaptopurine; alkaloidic agents such as taxanes such as paclitaxel and docetaxel, vincristine and vinblastine; topoisomerase inhibitors such as camptothecins and amsacrine; Antibiotics such as anthracycline glycosides such as doxorubicin, daunorubicin, idarubicin, pirarubicin, and epirubicin; mytomycin; polyamine biosynthesis inhibitors such as eflornithine; mycophenolic acid and other inosine monophosphate dehydrogenase inhibitors; and anthrapyrazoles such as mitoxantrone, piroxantrone, and losoxantron
  • FOLFOX The current standard surgical adjuvant treatment for colorectal cancer comprising modified TNM Stage III or higher is FOLFOX 4.
  • FOLFOX combines oxaliplatin, leucovorin, and infusional 5FU.
  • Leucovorin is a drug that is used to enhance the anti-cancer effect of chemotherapy, and especially 5FU.
  • Other therapies uses are XELOX, a combination therapy comprising oxaliplatin and capecitabine; and FOLFIRI, which combines 5-FU, leucovorin, and irinotecan, a topoisomerase 1 inhibitor.
  • antibody-based therapeutics including but not limited to bevacizumab, which inhibits angiogenesis, cetuximab, an Epidermal Growth Factor Receptor inhibitor, and panitumumab, an Epidermal Growth Factor receptor inhibitor.
  • a cancer that originates in the colon or rectum is termed a colorectal cancer or bowel cancer.
  • Said cancer comprises colon cancer and rectal cancer.
  • a colorectal cancer according to the invention relates to a colon cancer.
  • a colorectal cancer according to the invention relates to a rectal cancer.
  • the invention provides a method for typing colorectal cancer cells according to the invention to select patients having an increased chance of responding to therapy.
  • a method of the invention can be instrumental for identifying subsets of colorectal cancer patients who are at risk for certain complications or who preferentially benefit from specific treatments. Information about colorectal subtypes could also substantially improve the design of future colorectal clinical studies by improving patient selection, reducing variability, and focusing on relevant outcome measures.
  • the invention provides a method of developing a colorectal gene signature for typing an RNA sample of an individual suffering from colorectal cancer or suspected of suffering there from, comprising determining a set of genes associated with a distant metastasis free survival period in RNA samples obtained from non-microsatellite instability (non-MSI) colorectal cancers, whereby said distant metastasis free period is 2 years, more preferred 3 years, more preferred 4 years, more preferred 5 years, more preferred more than 5 years.
  • Said non-MSI colorectal cancers preferably do not comprise low-level microsatellite instability (MSI-L) colorectal samples.
  • MSI is often caused by mutations in one of the mismatch repair genes MLH1, MSH2, MSH6, or PMS2 and results in high-level microsatellite instability (MSI-high) in tumours of patients.
  • An MSI test is based on mutation analyses in said mismatch repair genes.
  • the invention preferably provides a method of developing a colorectal gene signature for typing an RNA sample of an individual suffering from colorectal cancer or suspected of suffering there from, comprising determining a set of genes associated with a distant metastasis free survival period in RNA samples obtained from colorectal cancer samples have a valine at position 600 of B-Raf, whereby said distant metastasis free period is 2 years, more preferred 3 years, more preferred 4 years, more preferred 5 years, more preferred more than 5 years.
  • the invention provides an array, comprising between 5 and 12.000 nucleic acid molecules comprising a first set of nucleic acid molecules wherein each nucleic acid molecule of said first set comprises a nucleotide sequence that is able to hybridize to a different gene selected from the genes listed in Table 1.
  • an array according to the invention further comprises a second set of nucleic acid molecules wherein each nucleic acid molecule of said second set comprises a nucleotide sequence that is able to hybridize to normalization gene, whereby it is preferred that the RNA levels of said normalization genes are dissimilar.
  • the invention provides the use of an array according to the invention for obtaining a colorectal expression profile.
  • B-Raf mutations were analyzed in exon 15 after amplification of cDNA to detect a V600E activating mutation.
  • Primers used were (primer 1) 5'-tgatcaaacttatagatattgcacga and (primer 2) 5'-tcatacagaacaattccaaatgc.
  • Amplified products were purified using a Macherey-Nagel NucleoFast® purification kit. Samples comprising a V600E activating mutation in B-Raf were to a large extent removed from the training set of samples.
  • RNA samples Aliquots of total RNA from frozen tumor samples were available for this study. Two-hundred nanogram total RNA was amplified using the Low RNA Input Fluorescent Labeling Kit (Agilent Technologies). Cyanine 3-CTP or Cyanine 5-CTP (GE Health Care) was directly incorporated into the cRNA during in vitro transcription. A total of 750 ng of Cyanine-labeled RNA was co-hybridized with a standard reference to Agilent 44k oligo nucleotide microarrays at 60 degrees Celsius for 17 hrs and subsequently washed according to the Agilent standard hybridization protocol (Agilent Oligo Microarray Kit, Agilent Technologies). Said standard reference (colon reference pool) comprised 44 colorectal cancer samples, of which 13 were obtained from patients who developed metastasis within 5 years after surgery, and 31 were obtained from patients who did not develop metastasis within 5 years after surgery.
  • the 18 identified genes were used to construct a colon prognosis classifier that is analogous to a previous defined, breast cancer prognosis signature ( W02002103320 ; which is hereby incorporated by reference). For each sample, a low-risk score and a high-risk score was calculated based on the 18-gene expression pattern in that sample. Both scores were combined into a final index. The optimal threshold for the classifier index score was determined in such a way to reach optimal sensitivity and specificity. If a sample's index exceeded a threshold (-0.05) it was considered as a high-risk samples, and visa versa.
  • the 18-gene profile was validated on an independent cohort of 178 stage II and III colon samples.
  • the profile classified 61% of the validation samples as low-risk and 39% as high-risk.
  • Five-year DMFS rates were 89% (95CI, 93-95%) for low-risk and 62% (95CI, 50-77%) for high-risk samples.
  • Treatment benefit on low-risk and high-risk patients within validation cohort A treatment benefit of chemotherapy was determined by analysis of the 5-year DM development rates of treated vs. untreated 18-gene low-risk and high-risk patients. Treatment benefit was absent from patients classified as low-risk (stage II/III, -0% DM; stage II, +2.7% DM). Treatment benefit on high-risk patients was observed (stage II/III, -10.4% DM; stage II, -9.5% DM). These results ( Figure 6 ) indicate that high-risk patients are more likely to benefit from chemotherapy.
  • the prognostic power of a two-gene prognosis model was exemplified using MCTP1 and THNSL2 genes.
  • Validation samples with a high MCTP1/THNSLC2 ratio showed a 5-year DMFS of 87% (95CI, 80-95%) and samples with a low MCTP1/THNSLC2 ratio (high-risk) showed a DMFS of 70% (95CI, 60-82%).
  • Table 1 18-set 38/4 4-set Sequence Gene Name Systematic Name SEQ ID NO y y TTAGAAGAGATGGCTTATTAACAGGGAAGAAGCTTGTTATATTCCAGTTGTAAGAATAGC ZBED4 NM_014838 1 y y CATTTCCCTGCAGATGGTACAGATGTTCCTGCCTTAGAGTCATCTCTAGTTCCCCACCTC LIF NM_002309 2 y GGGAGCCTTCTTGATGATCTCAAAAATAATAGCTATTCAAGAAAATCACCAAGTGACTGT IL18R1 NM_003855 3 y y AGCCTGAGCGTTTAATTTATTCAGTACCTGTGTTTGTGTGAATGCGGTGTGTGCAGGCAT PIM3 NM_001001852 4 TTTTGAAGAAAAAGTCCTTCACTTTTCCAAGAGACCATACGTCAGTTACAACTAATACAG PYROXD1 NM_024854 5 TCCATATCTTTGTTTTAACCAGTACTTCTAAGAGCAT

Abstract

The invention relates to a method of typing colorectal cancer cells by determining the RNA levels of a set of signature genes. Said typing can be use for predicting a risk for recurrence of said colorectal cancer. The invention further relates to a set of genes that can be used for normalizing the RNA levels of said set of signature genes, and to micro-array comprising said set of signature genes.

Description

  • The invention relates to the field of oncology. More specifically, the invention relates to a method for typing colorectal cancer cells. The invention provides means and methods for differentiating colorectal cancer cells with a low metastasizing potential and with a high metastatic potential.
  • Worldwide over a million new cases of colorectal cancer were diagnosed in 2002, accounting for more than 9% of all new cancer cases (Ries et al., editors. National Cancer Institute Bethesda, MD. 2006. 5-3-2006. SEER Cancer Statistics Review, 1975-2003). Colorectal cancer is the third most common cancer worldwide after lung and breast with two-thirds of all colorectal cancers occurring in the more developed regions. As with all cancers, chances of survival are good for patients when the cancer is detected in an early stage. Stage I patients have a survival rate of ∼93% while the 5-year survival rate drops to ∼80% in stage II patients and to 60% in stage III patients (Sobrero et al., 2006. The Lancet Oncology 7(6): 515-517).
  • Despite numerous clinical trials, the benefit of adjuvant chemotherapy for stage II colon cancer patients is still debatable (Andre et al., 2006. Annals of Surgical Oncology 13(6): 887-898). Several analyses and meta-analyses have been performed of clinical trials comparing adjuvant therapy with observation in patients with stage II colon or colorectal cancer (for review, see Benson et al., 2004. Journal of Clinical Oncology 22: 3408-3419). Three-fourth of patients is cured by surgery alone and therefore, less than 25% of patients would benefit from additional chemotherapy. As a result, the number of patients receiving adjuvant chemotherapy varies significantly amongst developed countries and the official guidelines give no clear recommendation (Van Cutsem et al., 2005. Annals of Oncology 16(suppl_1):i18-i19). For stage III patients, adjuvant treatment is recommended for all patients (Gill et al., 2004. Journal of Clinical Oncology 22: 1797-1806) although patients with T1 or T2 N1 MO tumors (stage IIIA) have a significantly better survival rate than stage II B patients indicating that many patients would not require additional chemotherapy.
  • The identification of the sub-group of patients that are more likely to suffer from a recurrent disease would therefore allow the identification of patients who are more likely to benefit from adjuvant treatment after surgery. Much effort has been put on the identification of clinico-pathological parameters that predict prognosis. The most important factors for predicting the risk of recurrence are emergency presentation, poorly differentiated tumor (histological grade) and depth of tumor invasion and adjacent organ involvement (T4) (Van Cutsem et al., 2005. Annals of Oncology 16(suppl_1):i18-i19; Le Voyer et al., 2003. Journal of Clinical Oncology 21: 2912-2919). Assessment of an inadequate number of lymph node is an additional risk factor as low numbers of examined lymph nodes is associated with a decreased 5-year survival rate. Although these clinical parameters have been shown to correlate to outcome, physicians acknowledge that they are insufficient to correctly identify high risk patients.
  • Current pathological prediction factors are not sufficient to identify "high risk" patients, who have an increased risk for recurrent disease. It is therefore an object of the present invention to provide methods and means to allow typing of cancer samples from patients suffering from colorectal cancer to identify said high risk patients and low risk patients.
  • Therefore, the invention provides a method for typing a RNA sample of an individual suffering from colorectal cancer or suspected of suffering there from, the method comprising providing an RNA sample that is prepared from a tissue sample from said individual, said tissue sample comprising colorectal cancer cells or suspected to comprise colorectal cancer cells; determining RNA levels for a set of genes in said RNA sample; and typing said RNA sample on the basis of the RNA levels determined for said set of genes; wherein said set of genes comprises at least two of the genes listed in Table 1.
  • This study discloses a robust gene expression signature that predicts disease relapse and be added to current clinicopathological risk assessment to assist physicians in making treatment decisions. The identification of the sub-group of patients that are more likely to suffer from a recurrent disease allows the identification of patients who are more likely to benefit from adjuvant chemotherapy and should be treated after surgery.
  • The present gene expression signature was identified after removing to a large extent training samples comprising cancer cells with an activating mutation in B-Raf (BRAFmut). BRAFmut colon cancer samples were found to be highly variable in gene expression data which masked more general, prognosis-related gene expression data. Without being bound by theory, said variable gene expression might be caused by a high degree of micro-satellite instability (MSI) in BRAFmut colon cancer samples. The resultant gene expression signature was found to be robust and applicable to a sample comprising cancer cells with and without BRAFmut.
  • Colorectal cancer is a type of cancer that originates in the large intestine or bowel, comprising the colon and the rectum. Colon cancer and rectal cancer have many features in common. The majority of colorectal cancers are adenocarcinomas. These are cancers of the cells that line the inside layer of the wall of the colon and rectum. Other less common types of tumors may also develop in the colon and rectum, such as carcinoid tumors, which develop from specialized hormone-producing cells of the intestine; gastrointestinal stromal tumors or leiomyosarcomas, which develop from smooth muscle cells in the wall of the intestine; and lymphomas, which are cancers of immune system cells that typically develop in lymph nodes but also may start in the colon and rectum or other organs.
  • Adenocarcinomas usually start as a colorectal polyp, a hyperplasia which is defined as a visible protrusion above the surface of the surrounding normal large bowel mucosa. Colorectal polyps are classified as either neoplastic (adenomatous polyps) or non-neoplastic, comprising hyperplastic, mucosal, inflammatory, and hamartomatous polyps which have no malignant potential. Adenomatous polyps, or adenomas, are attached to the bowel wall by a stalk (pedunculated) or by a broad, flat base (sessile). A colorectal hyperplasia or polyp can develop into a malignant adenocarcinoma.
  • Using RNA isolated from a training set of colorectal samples with a wild type B-Raf gene and comprising samples from colorectal cancers that did not give rise to metastases in patients within the length of follow up time of each patient; and samples from colorectal cancers that gave rise to metastases in patients within the length of follow up time of each patient, genes were selected using a multivariate Cox Regression based method (Simon et al., Design and Analysis of DNA Microarray Investigations, Springer-Verlag New York, (2003); Korn et al.,. Journal of Statistical Planning and Inference 124, 379-398 (2004)). Genes were selected of which the RNA levels was significantly related to survival of the patient, independent of patient stage, where survival is defined as being free of cancer recurrence. Each of the genes listed in Table 1 was shown to be predictive of survival and have a minimum significance threshold of 0.001.
  • In a preferred embodiment, a set of at least two genes comprises MCTP1 (SEQ ID NO 36) and THNSL2 (SEQ ID NO 13). More preferred is the determination of a ratio of expression of MCTP1 (SEQ ID NO 36) and THNSL2 (SEQ ID NO 13). A sample with a determined MCTP1/THNSLC2 ratio above a predetermined threshold is indicative of a sample with a low risk of cancer recurrence. Samples with a high MCTP1/THNSLC2 ratio (low-risk) showed a 5-year distant metastasis free survival (DMSF) of 87%. Samples with a low MCTP1/THNSLC2 ratio (high-risk) showed a DMFS of 70%.
  • In a preferred embodiment, a set of genes according to the invention comprises at least three of the genes listed in Table 1, more preferred at least four of the genes listed in Table 1, more preferred at least five of the genes listed in Table 1, more preferred at least six of the genes listed in Table 1, more preferred at least seven of the genes listed in Table 1, more preferred at least eight of the genes listed in Table 1, more preferred at least nine of the genes listed in Table 1, more preferred at least ten of the genes listed in Table 1, more preferred at least fifteen of the genes listed in Table 1, more preferred at least twenty of the genes listed in Table 1, more preferred at least twenty-five of the genes listed in Table 1, more preferred at least thirty of the genes listed in Table 1, more preferred at least forty of the genes listed in Table 1, more preferred at least fifty of the genes listed in Table 1, more preferred at least sixty of the genes listed in Table 1, more preferred at least seventy of the genes listed in Table 1, more preferred at least eighty of the genes listed in Table 1, more preferred hundred of the genes listed in Table 1, more preferred hundred-fifty of the genes listed in Table 1, more preferred two-hundred of the genes listed in Table 1, more preferred all of the genes listed in Table 1.
  • A preferred set of genes for use in a method of the invention comprises the first two rank-ordered genes listed in Table 1, more preferred the first three rank-ordered genes, more preferred the first four rank-ordered genes, more preferred the first five rank-ordered genes, more preferred the first six rank-ordered genes, more preferred the first seven rank-ordered genes, more preferred the first eight rank-ordered genes, more preferred the first ten rank-ordered genes, more preferred the first fifteen rank-ordered genes, more preferred the first twenty rank-ordered genes, more preferred the first thirty rank-ordered genes, more preferred the first fourty rank-ordered genes, more preferred the first fifty rank-ordered genes, more preferred the first sixty rank-ordered genes, more preferred the first seventy rank-ordered genes, more preferred the first eighty rank-ordered genes, more preferred the first ninety rank-ordered genes, more preferred the first hundred rank-ordered genes, more preferred the first hundred-fifty rank-ordered genes, more preferred the first two-hundred rank ordered genes, more preferred all two hundred and nine genes listed in Table 1.
  • A preferred signature comprises genes referred to in Table 1 as ZBED4, LIF, PIM3, IL2RA, PYROXD1, CTSC, EDEM1, M6PRBP1, SLC6A12, THNSL2, PPARA, ZNF697, LAMA3, CA438802, MCTP1, HSD3B1, CYFIP2, IL2RB.
  • A further preferred signature comprises genes referred to in Table 1 as ZBED4, LIF, IL18R1, PIM3, IL2RA, PYROXD1, CTSC, EDEM1, M6PRBP1, SLC6A12, THNSL2, KCNJ10, THC2663361, C10orf67, KIAA0040, BC040628, AK096685, PIGW, PPARA, COLQ, AK021427, C15orf27, PRDM4, LOC165186, ZNF697, CRYGA, EEPD1, LAMA3, NEDD8, CA438802, MCTP1, HSD3B1, CYFIP2, IL2RB, XKR3, NT_035113, THC2520461, and THC2662025. -
  • A cell sample is a clinically relevant sample that comprises a colorectal cancer cell or an expression product comprising a nucleic acid from a colorectal cancer cell.
  • In a preferred embodiment, a cell sample according to the invention is obtained directly from the large intestine during surgery. In an alternative embodiment, the cell sample is prepared from a biopsy sample that is taken during colonoscopy.
  • It is further preferred that the biopsies have a depth of at most 10 millimeter, more preferred at most 5 millimeter, with a preferred diameter of about 2 millimeter, more preferred about 3 millimeter, more preferred about 4 millimeter, more preferred about 5 millimeter, more preferred about 6 millimeter, more preferred about 7 millimeter, more preferred about 8 millimeter, more preferred about 9 millimeter, more preferred about 10 millimeter. However, other forms that are equal in size and total volume are also possible.
  • In another preferred embodiment, the tissue sample comprises stool or blood voided by a patient suffering from colorectal cancer, said tissue sample comprising a colorectal cancer cell or a gene expression product such as a nucleic acid product from a colorectal cancer cell. Methods to purify cells or gene expression products such as RNA from human stool or blood samples are known in the art and have been described for example in patent application W0199820355 , W02003068788 , and Yang et al. 2005. Cancer Lett 226: 55-63, which are enclosed by reference.
  • Samples can be processed in numerous ways, as is known to a skilled person. For example, they can be freshly prepared from cells or tissues at the moment of harvesting, or they can be prepared from samples that are stored at -70°C until processed for sample preparation. Alternatively, tissues, biopsies, stool or blood samples can be stored under conditions that preserve the quality of the protein or RNA. Examples of these preservative conditions are fixation using e.g. formaline, RNase inhibitors such as RNAsin (Pharmingen) or RNasecure (Ambion), aquous solutions such as RNAlater (Assuragen; US06204375 ), Hepes-Glutamic acid buffer mediated Organic solvent Protection Effect (HOPE; DE10021390 ), and RCL2 (Alphelys; W004083369 ), and non-aquous solutions such as Universal Molecular Fixative (Sakura Finetek USA Inc.; US7138226 ).
  • The RNA level of at least two of the genes listed in Table 1 can be determined by any method known in the art. Methods to determine RNA levels of genes are known to a skilled person and include, but are not limited to, Northern blotting, quantitative PCR, and microarray analysis.
  • Northern blotting comprises the quantification of the nucleic acid expression product of a specific gene by hybridizing a labeled probe that specifically interacts with said nucleic acid expression product, after separation of nucleic acid expression products by gel electrophoreses. Quantification of the labeled probe that has interacted with said nucleic acid expression product serves as a measure for determining the level of expression. The determined level of expression can be normalized for differences in the total amounts of nucleic acid expression products between two separate samples by comparing the level of expression of a gene that is known not to differ in expression level between samples.
  • Quantitative Polymerase Chain Reaction (qPCR) provides an alternative method to quantify the level of expression of nucleic acids. qPCR can be performed by real-time PCR (rtPCR), in which the amount of product is monitored during the reaction, or by end-point measurements, in which the amount of a final product is determined. As is known to a skilled person, rtPCR can be performed by either the use of a nucleic acid intercalator, such as for example ethidium bromide or SYBR® Green I dye, which interacts which all generated double stranded products resulting in an increase in fluorescence during amplification, or by the use of labeled probes that react specifically with the generated double stranded product of the gene of interest. Alternative detection methods that can be used are provided by dendrimer signal amplification, hybridization signal amplification, and molecular beacons.
  • Different amplification methods, known to a skilled artisan, can be employed for qPCR, including but not limited to PCR, rolling circle amplification, nucleic acid sequence-based amplification, transcription mediated amplification, and linear RNA amplification.
  • For the simultaneous detection of multiple nucleic acid gene expression products, qPCR methods such as reverse transcriptase- multiplex ligation-dependent amplification (rtMLPA), which accurately quantifies up to 45 transcripts of interest in a one-tube assay (Eldering et al., Nucleic Acids Res 2003; 31: e153) can be employed.
  • Microarray-based analyses involve the use of selected biomolecules that are immobilized on a surface. A microarray usually comprises nucleic acid molecules, termed probes, which are able to hybridize to nucleic acid expression products. The probes are exposed to labeled sample nucleic acid, hybridized, and the abundance of nucleic acid expression products in the sample that are complementary to a probe is determined. The probes on a microarray may comprise DNA sequences, RNA sequences, or copolymer sequences of DNA and RNA. The probes may also comprise DNA and/or RNA analogues such as, for example, nucleotide analogues or peptide nucleic acid molecules (PNA), or combinations thereof. The sequences of the probes may be full or partial fragments of genomic DNA. The sequences may also be in vitro synthesized nucleotide sequences, such as synthetic oligonucleotide sequences.
  • It is preferred that said RNA levels are determined simultaneously. Simultaneous analyses can be performed, for example, by multiplex qPCR and microarray analysis. Microarray analyses allow the simultaneous determination of the nucleic acid levels of expression of a large number of genes, such as more than 50 genes, more than 100 genes, more than 1000 genes, or even more than 10.000 genes, allowing the use of a large number of gene expression data for normalization of the genes comprising the colorectal expression profile.
  • In a preferred embodiment, therefore, said RNA levels are determined by microarray analysis.
  • Said probe is specific for a gene listed in Table 1. A probe can be specific when it comprises a continuous stretch of nucleotides that are completely complementary to a nucleotide sequence of a RNA product of said gene, or a cDNA product thereof. A probe can also be specific when it comprises a continuous stretch of nucleotides that are partially complementary to a nucleotide sequence of a RNA product of said gene, or a cDNA product thereof. Partially means that a maximum of 5% from the nucleotides in a continuous stretch of at least 20 nucleotides differs from the corresponding nucleotide sequence of a RNA product of said gene. The term complementary is known in the art and refers to a sequence that is related by base-pairing rules to the sequence that is to be detected. It is preferred that the sequence of the probe is carefully designed to minimize nonspecific hybridization to said probe. It is preferred that the probe is or mimics a single stranded nucleic acid molecule. The length of said complementary continuous stretch of nucleotides can vary between 15 bases and several kilo bases, and is preferably between 20 bases and 1 kilobase, more preferred between 40 and 100 bases, and most preferred 60 nucleotides. A most preferred probe comprises a continuous stretch of 60 nucleotides that are identical to a nucleotide sequence of a RNA product of a gene, or a cDNA product thereof.
  • To determine the RNA level of at least two of the genes listed in Table 1, the RNA sample is preferably labeled, either directly or indirectly, and contacted with probes on the array under conditions that favor duplex formation between a probe and a complementary molecule in the labeled RNA sample. The amount of label that remains associated with a probe after washing of the microarray can be determined and is used as a measure for the level of RNA of a nucleic acid molecule that is complementary to said probe.
  • The determined RNA levels for at least two genes listed in Table 1 can be normalized to correct for systemic bias. Systemic bias results in variation by inter-array differences in overall performance, which can be due to for example inconsistencies in array fabrication, staining and scanning, and variation between labeled RNA samples, which can be due for example to variations in purity. Systemic bias can be introduced during the handling of the sample in a microarray experiment. To reduce systemic bias, the determined RNA levels are preferably corrected for background non-specific hybridization and normalized using, for example, Feature Extraction software (Agilent Technologies). Other methods that are or will be known to a person of ordinary skill in the art, such as a dye swap experiment (Martin-Magniette et al., Bioinformatics 21:1995-2000 (2005)) can also be applied to normalize differences introduced by dye bias. Normalization of the expression levels results in normalized expression values.
  • Conventional methods for normalization of array data include global analysis, which is based on the assumption that the majority of genetic markers on an array are not differentially expressed between samples [Yang et al., Nucl Acids Res 30: 15 (2002)]. Alternatively, the array may comprise specific probes that are used for normalization. These probes preferably detect RNA products from housekeeping genes such as glyceraldehyde-3-phosphate dehydrogenase and 18S rRNA levels, of which the RNA level is thought to be constant in a given cell and independent from the developmental stage or prognosis of said cell.
  • Therefore, a preferred method according to the invention further comprises normalizing the determined RNA levels of said set of at least two of the genes listed in Table 1 in said sample.
  • Said normalization preferably comprises median centering, in which the "centers" of the array data are brought to the same level under the assumption that the majority of genes are un-changed between conditions. Said normalization preferably comprises Lowess (LOcally WEighted Scatterplot Smoothing) local regression normalization to correct for both print-tip and intensity-dependent bias.
  • In a preferred embodiment, genes are selected of which the RNA levels are largely constant between different tissue samples comprising colorectal cells from one individual, and between tissue samples comprising colorectal cells from different individuals. It is furthermore preferred that RNA levels of said set of normalization genes differ between the genes. For example, it is preferred to select genes with a low RNA level in said tissue sample, and genes with a high RNA level. More preferred is to select genes with a low RNA level in said tissue sample, genes with a moderate RNA level, and genes with a high RNA level. It will be clear to a skilled artisan that the RNA levels of said set of normalization genes preferably allow normalization over the whole range of RNA levels.
  • A preferred method further comprises multiplying each of the normalized expression values with a predetermined constant for said gene to obtain a weighted value for the relative RNA level of said gene, and thereby a set of weighted values for said set of genes, said method further comprising typing said sample on the basis of said set of weighted values.
  • Said set of weighted values can be summed and compared to a summed set of weighted values from a reference sample. It is preferred that said summed set of weighted values is compared to a classification threshold, that is determined by the values obtained from RNA samples of which the typing is known.
  • Colorectal cancers such as adenocarcinomas are staged dependent on the visible invasiveness of the surrounding tissue. A staging system is provided by the TNM Staging System, which combines data about the Tumor (T), the spread to lymph nodes (N), and the existence of distant metastases (M). A TNM stage I colorectal cancer is defined as a cancer that began to spread and has invaded the submucosa or the muscularis propria. A. TNM stage II defines a cancer that has invaded through the muscularis propria into the subserosa, or into the pericolic or perirectal tissues, but has not reached the lymph nodes. A stage III defines a cancer that has spread to the lymph nodes in the absence of distant metastases. A stage IV defines a cancer that has spread to distant sites.
  • In a preferred embodiment, the invention provides a method of typing an individual suffering from colorectal cancer, wherein said colorectal cancer comprises a TNM stage I, TNM stage II or TNM stage III colorectal cancer as determined by the TNM Staging System, wherein TNM stage II and TNM stage III are preferred colorectal cancers.
  • It is preferred that said typing in a method according to the invention allows differentiating cancer cells with a low metastasizing potential or risk of cancer recurrence and cancer cells with a high metastatic potential or risk of cancer recurrence.
  • To differentiate cancer cells with a low metastasizing potential and cancer cells with a high metastatic potential, the RNA levels at least two of the genes listed in Table 1 can be compared to RNA levels of said genes in a reference sample.
  • A reference sample is preferably an RNA sample isolated from a colorectal tissue from a healthy individual, or an RNA sample from a relevant cell line or mixture of cell lines. Said reference sample can also be an RNA sample from a cancerous growth of an individual suffering from colorectal cancer. Said individual suffering from colorectal cancer can have an increased risk of cancer recurrence, or a low risk of cancer recurrence.
  • It is preferred that said reference sample is an RNA sample from an individual suffering from colorectal cancer and having a low risk of cancer recurrence. In a more preferred embodiment, said reference sample is a pooled RNA sample from multiple tissue samples comprising colorectal cells from individuals suffering from colorectal cancer and having a low risk of cancer recurrence. It is preferred that said multiple tissue sample comprises more than 10 tissue samples, more preferred more than 20 tissue samples, more preferred more than 30 tissue samples, more preferred more than 40 tissue samples, most preferred more than 50 tissue samples. A most preferred reference sample comprises pooled RNA from multiple tissue samples comprising colorectal cancer cells from individuals having a low risk of cancer recurrence and from individuals having a high risk of cancer recurrence.
  • A further preferred reference sample comprises RNA isolated and pooled from colon tissue from healthy individuals, or from so called normal adjacent tissue from colon cancer patients or RNA from a generic cell line or cell line mixture. The RNA from a cell line or cell line mixture can be produced in-house or obtained from a commercial source such as, for example, Stratagene Human Reference RNA.
  • Typing of a sample can be performed in various ways. In one method, a coefficient is determined that is a measure of a similarity or dissimilarity of a sample with said reference sample. A number of different coefficients can be used for determining a correlation between the RNA expression level in an RNA sample from an individual and a reference sample. Preferred methods are parametric methods which assume a normal distribution of the data. One of these methods is the Pearson product-moment correlation coefficient, which is obtained by dividing the covariance of the two variables by the product of their standard deviations. Preferred methods comprise cosine-angle, un-centered correlation and, more preferred, cosine correlation (Fan et al., Conf Proc IEEE Eng Med Biol Soc. 5:4810-3 (2005)).
  • Preferably, said correlation with a reference sample is used to produce an overall similarity score for the set of genes that are used. A similarity score is a measure of the average correlation of RNA levels of a set of genes in an RNA sample from an individual and a reference sample. Said similarity score can, for example, be a numerical value between +1, indicative of a high correlation between the RNA expression level of the set of genes in a RNA sample of said individual and said reference sample, and -1, which is indicative of an inverse correlation and therefore indicative of having an increased risk of cancer recurrence (van 't Veer et al., Nature 415: 484-5 (2002)).
  • In another aspect, the invention provides a method of classifying an individual suffering from colorectal cancer, comprising classifying said individual as having a poor prognosis or a good prognosis by a method comprising determining a similarity value between RNA levels from a set of at least two genes listed in Table 1 in a RNA sample from said individual and a level of expression from said set of genes in a RNA sample from a patient having no recurrent disease within five years of initial diagnosis, and classifying said individual as having a poor prognosis if said similarity value is below a similarity threshold value, and classifying said individual as having a good prognosis if said similarity value exceeds a similarity threshold value.
  • The present invention provides a set of markers useful for distinguishing samples from colorectal cancer patients with a good prognosis from samples from colorectal cancer patients with a poor prognosis. In a method of the invention the expression level of these markers is used to determine whether an individual afflicted with colon cancer will have a good or poor clinical prognosis. In one embodiment, the invention provides for a method of determining whether an individual afflicted with colon cancer will likely experience a relapse within five years of initial diagnosis (i. e., whether an individual has a poor prognosis) comprising (1) comparing the level of expression of at least two of the genes listed in Table 1 in a sample taken from the individual to the level of the same markers in a control, where the levels of said control represent those found in an individual with a poor prognosis; and (2) determining whether the level of the expression of each gene from said at least two genes in the sample from the individual is significantly different from the control. If no substantial difference is found, the patient has a poor prognosis, and if a substantial difference is found, the patient has a good prognosis. Persons of skill in the art will readily see that said control levels may alternatively represent those found in an individual with a good prognosis. In a more specific embodiment, both controls are run. In case the pool is not pure 'good prognosis' or 'poor prognosis', a set of experiments of individuals with known outcome should be hybridized against the pool to define the expression control levels for the good prognosis and poor prognosis group. Each individual with unknown outcome is hybridized against the same pool and the resulting expression profile is compared to the templates to predict its outcome.
  • Poor prognosis of colon cancer may indicate that a tumor is relatively aggressive, while good prognosis may indicate that a tumor is relatively non-aggressive.
  • Therefore, the invention provides for a method of determining a course of treatment of a colon cancer patient, comprising determining whether the level of expression of at least two genes of table 1 correlates with the level of these genes in a sample representing a good prognosis expression pattern or a poor prognosis pattern; and determining a course of treatment, wherein if the expression correlates with the poor prognosis pattern, the tumor is treated as an aggressive tumor.
  • A preferred method of classifying a sample as either high or low risk for disease recurrence involves the use of a classification template, derived from Support Vector Machine (SVM) training using all genes identified as being correlated with disease progression. Each gene in the template (signature) has a corresponding weighing factor, as determined by the SVM implementation by Chang & Lin (Chih-Chung Chang and Chih-Jen Lin, LIBSVM: a library for support vector machines, 2001. http://www.csie.ntu.edu.tw/∼cjlin/libsvm). This algorithm analyses the information contained in the signature genes across all training set samples and constructs a classification template that best separates patients with recurrence from those without. LIBSVM, developed by Chih-Chung Chang and Chih-Jen Lin, is an integrated software for analyzing many problems in supervised classification or regression frameworks.
  • A similarity threshold value is an arbitrary value that allows discriminating between RNA samples from patients with a high risk of cancer recurrence, and RNA samples from patients with a low risk of cancer recurrence.
  • Said similarity threshold value is set at a value at which an acceptable number of patients with known metastasis formation within five years after initial diagnosis would score as false negatives above the threshold value, and an acceptable number of patients without known metastasis formation within five years after initial diagnosis would score as false positives below the threshold value.
  • A similarity score is preferably displayed or outputted to a user interface device, a computer readable storage medium, or a local or remote computer system.
  • In an alternative embodiment the invention provides a method of classifying an individual suffering from colorectal cancer, comprising classifying said individual as having a poor prognosis or a good prognosis by a method comprising (a) providing an RNA sample from a said individual that is prepared from a tissue sample from said individual, said tissue sample comprising colorectal cancer cells or suspected to comprise colorectal cancer cells; (b) determining a level of RNA for a set of genes comprising at least two of the genes listed in Table 1 in said sample; (c) determining a similarity value between a level of expression from the set of genes in said individual and a level of expression from said set of genes in a patient having no recurrent disease within five years of initial diagnosis; and (d) classifying said individual as having a poor prognosis if said similarity value is below a first similarity threshold value, and classifying said individual as having a good prognosis if said similarity value exceeds said first similarity threshold value.
  • In a preferred method of the invention, the level of RNA for a set of genes comprising at least two of the genes listed in Table 1 in said sample is normalized. Normalization can be performed by any method known to a skilled artisan, including global analysis and the use of specific probes.
  • In yet another aspect, the invention provides a method of assigning treatment to an individual suffering from colorectal cancer, comprising classifying said individual as having a poor prognosis or a good prognosis according to a method of the invention, and assigning adjuvant chemotherapy if said individual is classified as having poor prognosis.
  • A routine treatment for colorectal cancer is surgery, which is followed by additional treatment if said individual is classified as having poor prognosis. Said additional treatment is selected from adjuvant chemotherapy and radiotherapy. Chemotherapy comprises the use of natural or non-natural compounds to eliminate fast-dividing, and therefore susceptible, cancer cells. Chemotherapeutic compounds comprise alkylating agents such as decarbazine and cyclophosphamide; DNA crosslinking agents such as cisplatin and carboplatin; antimetabolitic agents such as methotrexate, 5-fluorouracil (5FU), and mercaptopurine; alkaloidic agents such as taxanes such as paclitaxel and docetaxel, vincristine and vinblastine; topoisomerase inhibitors such as camptothecins and amsacrine; Antibiotics such as anthracycline glycosides such as doxorubicin, daunorubicin, idarubicin, pirarubicin, and epirubicin; mytomycin; polyamine biosynthesis inhibitors such as eflornithine; mycophenolic acid and other inosine monophosphate dehydrogenase inhibitors; and anthrapyrazoles such as mitoxantrone, piroxantrone, and losoxantrone.
  • The current standard surgical adjuvant treatment for colorectal cancer comprising modified TNM Stage III or higher is FOLFOX 4. FOLFOX combines oxaliplatin, leucovorin, and infusional 5FU. Leucovorin is a drug that is used to enhance the anti-cancer effect of chemotherapy, and especially 5FU. Other therapies uses are XELOX, a combination therapy comprising oxaliplatin and capecitabine; and FOLFIRI, which combines 5-FU, leucovorin, and irinotecan, a topoisomerase 1 inhibitor. These can be combined with antibody-based therapeutics including but not limited to bevacizumab, which inhibits angiogenesis, cetuximab, an Epidermal Growth Factor Receptor inhibitor, and panitumumab, an Epidermal Growth Factor receptor inhibitor.
  • A cancer that originates in the colon or rectum is termed a colorectal cancer or bowel cancer. Said cancer comprises colon cancer and rectal cancer. In a preferred embodiment, a colorectal cancer according to the invention relates to a colon cancer. In another preferred embodiment, a colorectal cancer according to the invention relates to a rectal cancer.
    In yet another aspect, the invention provides a method for typing colorectal cancer cells according to the invention to select patients having an increased chance of responding to therapy. A method of the invention can be instrumental for identifying subsets of colorectal cancer patients who are at risk for certain complications or who preferentially benefit from specific treatments. Information about colorectal subtypes could also substantially improve the design of future colorectal clinical studies by improving patient selection, reducing variability, and focusing on relevant outcome measures.
  • In a further aspect, the invention provides a method of developing a colorectal gene signature for typing an RNA sample of an individual suffering from colorectal cancer or suspected of suffering there from, comprising determining a set of genes associated with a distant metastasis free survival period in RNA samples obtained from non-microsatellite instability (non-MSI) colorectal cancers, whereby said distant metastasis free period is 2 years, more preferred 3 years, more preferred 4 years, more preferred 5 years, more preferred more than 5 years. Said non-MSI colorectal cancers preferably do not comprise low-level microsatellite instability (MSI-L) colorectal samples. MSI is often caused by mutations in one of the mismatch repair genes MLH1, MSH2, MSH6, or PMS2 and results in high-level microsatellite instability (MSI-high) in tumours of patients. An MSI test is based on mutation analyses in said mismatch repair genes. The invention preferably provides a method of developing a colorectal gene signature for typing an RNA sample of an individual suffering from colorectal cancer or suspected of suffering there from, comprising determining a set of genes associated with a distant metastasis free survival period in RNA samples obtained from colorectal cancer samples have a valine at position 600 of B-Raf, whereby said distant metastasis free period is 2 years, more preferred 3 years, more preferred 4 years, more preferred 5 years, more preferred more than 5 years.
  • In yet another aspect, the invention provides an array, comprising between 5 and 12.000 nucleic acid molecules comprising a first set of nucleic acid molecules wherein each nucleic acid molecule of said first set comprises a nucleotide sequence that is able to hybridize to a different gene selected from the genes listed in Table 1.
  • In a preferred embodiment, an array according to the invention further comprises a second set of nucleic acid molecules wherein each nucleic acid molecule of said second set comprises a nucleotide sequence that is able to hybridize to normalization gene, whereby it is preferred that the RNA levels of said normalization genes are dissimilar.
  • In yet another aspect, the invention provides the use of an array according to the invention for obtaining a colorectal expression profile.
    • Figure legends
    • Figure 1: Unsupervised analysis identifies three colon subclasses.
    • Figure 2: Scoring of genes for their association with 5-year distant metastasis free survival (DMFS).
    • Figure 3: Kaplan Meier analysis of time to recurrence for 18-gene profile.
    • Figure 4: Kaplan Meier analysis of time to recurrence for 18-gene profile in stage II and III colon samples.
    • Figure 5: Kaplan Meier analysis of time to recurrence for 18-gene profile in treated and untreated colon samples
    • Figure 6: Treatment benefit on low-risk and high-risk patients within validation cohort.
    • Figure 7: Differentiation between samples classified as low-risk and high-risk by 18 gene profile.
    • Figure 8: Use of a MCTP1/THNSL2 ratio for colon prognosis.
    Examples Example 1 Generation of classifier Patients
  • Clinical and pathological information documented at the time of surgery included stage, grade, size and location of tumors. Additionally, the number of lymph nodes assessed for nodal involvement was described in 95% of cases. Tumors were staged according to the TMN staging system. All tissue samples were collected from patients with appropriate informed consent. The study was carried out in accordance with the ethical standards of the Helsinki Declaration and was approved by the Medical Ethical Board of the participating medical centers and hospitals. Patients were monitored for survival and recurrence for up to 270 months.
    • Mutational analysis
  • Mutation analysis was performed on all samples, including training set and validation set, using a sequencing approach. B-Raf mutations were analyzed in exon 15 after amplification of cDNA to detect a V600E activating mutation. Primers used were (primer 1) 5'-tgatcaaacttatagatattgcacga and (primer 2) 5'-tcatacagaacaattccaaatgc. Amplified products were purified using a Macherey-Nagel NucleoFast® purification kit. Samples comprising a V600E activating mutation in B-Raf were to a large extent removed from the training set of samples.
    • Microarray hybridization
  • Aliquots of total RNA from frozen tumor samples were available for this study. Two-hundred nanogram total RNA was amplified using the Low RNA Input Fluorescent Labeling Kit (Agilent Technologies). Cyanine 3-CTP or Cyanine 5-CTP (GE Health Care) was directly incorporated into the cRNA during in vitro transcription. A total of 750 ng of Cyanine-labeled RNA was co-hybridized with a standard reference to Agilent 44k oligo nucleotide microarrays at 60 degrees Celsius for 17 hrs and subsequently washed according to the Agilent standard hybridization protocol (Agilent Oligo Microarray Kit, Agilent Technologies).
    Said standard reference (colon reference pool) comprised 44 colorectal cancer samples, of which 13 were obtained from patients who developed metastasis within 5 years after surgery, and 31 were obtained from patients who did not develop metastasis within 5 years after surgery.
    • Microarray image analysis
  • Fluorescence intensities on scanned images were quantified, values corrected for background non-specific hybridization, and normalized using Agilent Feature Extraction software (Version 9.5.1.3) according to the manufactures recommended settings for the Agilent Whole Genome 44k microarray. The default normalisation procedure for this microarray includes a linear and a Lowess component, which corrects for any difference in Cy3/5 dye incorporation and centers the final profile at 0 (log10 scale, Cy5/Cy3). This process is described in the Agilent Feature Extraction Reference Guide.
    • Data pre-processing
  • Normalised gene expression ratios from each hybridisation were combined to produce a single gene expression profile, per patient, using Agendia XPrint software (version 1.5.1). To obtain a single expression ratio value for each of the signature genes on the array, an error-weighted mean value was calculated for the probes belonging to the same gene as log10 ratios. To establish appropriate relative weights, the Rosetta error model was used, which corrects for the uncertainties in individual probe measurements (Weng L et al, Bioinformatics 22:1111-21 (2006)). A text file containing normalised, error-weighted log ratios was generated, which was then used for further analysis. The data were then loaded into BRB ArrayTools (Simon et al., Cancer Informatics 2: 11-17 (2007)). To obtain a single expression ratio value for each unique probe on the array, a mean ratio value was calculated for all probes present more than once.
    • Prognostic gene selection
  • Unsupervised hierarchical clustering based on full-genome gene expression measurement indicated the existence of 3 main colon molecular subclasses (see Figure 1). Survival analysis of the three 3 classes showed that one subtype had a relative poor outcome (subtype C) and one subtype (subtype A) showed a good outcome (5-year distant metastasis free survival Hazard ratio A vs. C of 1.8, P=0.15). Further investigation of these subtypes indicated that both survival-associated subtypes, A and C, were enriched for samples with an activating BRAF mutation status (BRAFmut), especially for the good-outcome class (good-outcome class A: 52% BRAFmut, poor-outcome class C: 22% BRAFmut, compared to 4% for remaining subclass B). These finding suggested that samples within classes A and C showed a different gene expression pattern which is likely linked to the activated BRAF mutation phenotype. The BRAFmut subclasses were apparently enriched for colon samples with micro-satellite instability (MSI). The observed colon clustering might therefore represent the two known different colon tumor development pathways: MSS (subtype B) and MSI-derived (subtype A and perhaps also subtype C).
  • As cluster A and C can be discriminated based on full-genome unsupervised clustering, the differences between BRAFmut samples with a good and poor outcome are relative large. This large difference within BRAFmut samples might mask more general prognosis-related gene expression that is apparent for all colon subtypes, including subtype B, which consists for 96% (100/104) of wildtype BRAF samples with a mixed prognosis outcome. To circumvent the strong BRAFmut related gene expression differences, prognosis related gene expression was further investigated within subtype B samples only (n=104) and subsequently applied to all samples (n=188).
  • Using the "leave-one-out" cross validation procedure, all genes were scored for their association with 5-year distant metastasis free survival (DMFS). A set of 209 genes showed robust DMFS association in at least one iteration (Table 1), while 38 non-redundant probes (from a total set of 44 probes) showed robust DMFS association over 50% of all iterations (see Figure 2).
  • To ensure that the selected genes are optimally suited for diagnostic use and will result in equal readouts using a different array type and/or reference, we confirmed the expression measured on HD against the CRP reference to that on a different low-density (LD) array type and using a different reference (universal human cell line, UHR). Eighteen of the 38 probes could be matched to the LD and showed a highly correlative gene expression readout (R2>0.50) across 128 training samples that have been analyzed using both platforms. These 18 probes, corresponding to 18 genes or ORFs, were used for subsequent profile development (see Figure 7).
    • Example 2 Classifier training
  • The 18 identified genes were used to construct a colon prognosis classifier that is analogous to a previous defined, breast cancer prognosis signature ( W02002103320 ; which is hereby incorporated by reference). For each sample, a low-risk score and a high-risk score was calculated based on the 18-gene expression pattern in that sample. Both scores were combined into a final index. The optimal threshold for the classifier index score was determined in such a way to reach optimal sensitivity and specificity. If a sample's index exceeded a threshold (-0.05) it was considered as a high-risk samples, and visa versa. Survival analysis of the profile outcome on the training cohort (using a Leave One Out cross validation procedure) indicated a hazard ratio (HR) of 3.41 (P=1.4e-5) with a 5-year DMFS rate of 82% (95CI, 76-89%) for low-risk samples and 50% (95%CI, 38-66%) of high-risk samples. Disease-free survival is relative low for both high- and low-risk classes, likely because the great majority of samples within the training cohort did not receive adjuvant chemotherapy. Analysis separately for BRAF wildtype and BRAFmut samples confirmed that the 18-gene profile is independent from BRAF mutation status (Figure 3).
    • Example 3 Classifier evaluation
  • The 18-gene profile was validated on an independent cohort of 178 stage II and III colon samples. The profile classified 61% of the validation samples as low-risk and 39% as high-risk. The low- and high-risk samples showed a significant difference in DMFS with a HR of 3.19 (P=8.5e-4). Five-year DMFS rates were 89% (95CI, 93-95%) for low-risk and 62% (95CI, 50-77%) for high-risk samples.
  • In a multivariate analysis with both tumor stage and tumor grade, the 18-gene profile remained a robust prognostic factor with a HR of 2.95 (P=0.015) (tumor grade: HR=1.91, P=0.054; tumor stage: HR 1.61, P=0.35). The 18-gene profile showed a significant performance within stage II (P=0.0058) and III (P=0.036) only samples (Figure 4).
  • Next, we investigated whether the 18-gene profile showed prognostic power for samples from untreated patients only, or also for patients treated with chemotherapy. The 18-gene profile showed a significant performance for both untreated samples (P=0.0082), and treated patients (P=0.016) indicating that the performance of the profile is not caused due to treatment benefits (Figure 5).
    • Example 4
  • Treatment benefit on low-risk and high-risk patients within validation cohort A treatment benefit of chemotherapy was determined by analysis of the 5-year DM development rates of treated vs. untreated 18-gene low-risk and high-risk patients. Treatment benefit was absent from patients classified as low-risk (stage II/III, -0% DM; stage II, +2.7% DM). Treatment benefit on high-risk patients was observed (stage II/III, -10.4% DM; stage II, -9.5% DM). These results (Figure 6) indicate that high-risk patients are more likely to benefit from chemotherapy.
    • Example 5 MCTP1/THNSL2 ratio for colon prognosis
  • The prognostic power of a two-gene prognosis model was exemplified using MCTP1 and THNSL2 genes. A threshold for the MCTP1/THNSLC2 ratio was determined on the 188 training samples and showed a significant performance with a HR of 3.1 (P=6.8e-5). Samples with a high MCTP1/THNSLC2 ratio above the threshold were classified as low-risk. The MCTP1/THNSLC2 ratio model was confirmed on 178 independent validation samples and showed a significant HR of 2.3 (P=0.017) (Figure 8). Validation samples with a high MCTP1/THNSLC2 ratio (low-risk) showed a 5-year DMFS of 87% (95CI, 80-95%) and samples with a low MCTP1/THNSLC2 ratio (high-risk) showed a DMFS of 70% (95CI, 60-82%). Table 1
    18-set 38/4 4-set Sequence Gene Name Systematic Name SEQ ID NO
    y y TTAGAAGAGATGGCTTATTAACAGGGAAGAAGCTTGTTATATTCCAGTTGTAAGAATAGC ZBED4 NM_014838 1
    y y CATTTCCCTGCAGATGGTACAGATGTTCCTGCCTTAGAGTCATCTCTAGTTCCCCACCTC LIF NM_002309 2
    y GGGAGCCTTCTTGATGATCTCAAAAATAATAGCTATTCAAGAAAATCACCAAGTGACTGT IL18R1 NM_003855 3
    y y AGCCTGAGCGTTTAATTTATTCAGTACCTGTGTTTGTGTGAATGCGGTGTGTGCAGGCAT PIM3 NM_001001852 4
    TTTTGAAGAAAAAGTCCTTCACTTTTCCAAGAGACCATACGTCAGTTACAACTAATACAG PYROXD1 NM_024854 5
    TCCATATCTTTGTTTTAACCAGTACTTCTAAGAGCATAGAACTCAAATGCTGGGGGAGGT PPARA L02932 6
    y y AGAGAGGTTTCCGCAGAATAAAAAGCGGGTCACTCTATATGCTCTGTACAGGAAACTCTA IL2RA NM_000417 7
    y y TTTTGAAGAAAAAGTCCTTCACTTTTCCAAGAGACCATACGTCAGTTACAACTAATACAG PYROXD1 NM_024854 8
    y y AGTCGAAAAATCCCAAGGCCCAAACCTGCACCACTGACTGCTGAAATACAGCAAAAGATT CTSC NM_001814 9
    y y ATTACCACCTGTAATTCCTCTTTGGATTGTGTAGACTCAACATGAGACATTCCTTTCTGC EDEM1 NM_014674 10
    y y TCTCTATAATGCAGCTGTGCTCTGGAGTCCTCAACCCGGGGCTCATTTCAAACTTATTTT M6PRBP1 NM_005817 11
    y y GGAAGTGACAACTGAACACACTGTGTTGGATCGGAGGTTCCGTTAGGGGATCCTTCCTTA SLC6A12 NM_003044 12
    y y ACCCTGATGCGGAGAGGTGACAACTGGATGCTGATGCTTCGGGACACCATTGAGGACCTT THNSL2 NM_018271 13
    y AGGGACCTAGTGAAATCAATGAAACTCTTGAGTCTTGCTTAGGCTCGCAAACAAGAAGTG KCNJ10 NM_002241 14
    y AACAGAGGGCAGAAGGTCTATACGTCCTGAGGCCTTTTATGCAACGTTTGTTTGTGGAAT THC2663361 THC2663361 15
    y TGAAAAGCATTATCAACAGAATGAGGATAAGATGAGAAAATCCTTCAATCAGCAGTTAGC C10orf67 NM_153714 16
    y TGAAAATGAAAAGTCTTGATGTAGTCAGATGGTTACTCTCTTAACATTAGGTATTACCCC KIAA0040 XR_041165 17
    ACCCTGATGCGGAGAGGTGACAACTGGATGCTGATGCTTCGGGACACCATTGAGGACCTT THNSL2 NM_018271 18
    y AGAGGCCTTGAATACTCAGAAAATGGGAGATTGTGAATGGGTGTAGAGGATATCTATGAA BC040628 BC040628 19
    y AAGGAAAATGAATACTGTGTAATAGTTAAACCCATTCATAGGTTGCAATAGAGTGTCAGC AK096685 AK096685 20
    y GAAGCTTTTGTCAGTAACCTCAATGGAACCACCGTGCTGGAAATCACCCAGGGATTGTGC PIGW NM_178517 21
    AGCCTGAGCGTTTAATTTATTCAGTACCTGTGTTTGTGTGAATGCGGTGTGTGCAGGCAT PIM3 NM_001001852 22
    y y ACGGTTATTGACCCCATAGACTAGGGTAAGAATAAAGGCAATAAATTTGGTCTGACTCAG PPARA NM_005036 23
    y CCAAAACGCCATTGCCTTCCGCAGAGACCAGAGATCTCTGTACTTCAAGGACAGCCTTGG COLQ NM_080538 24
    y AAGAACTACCGGGAGACAAGAAAGGGACACTCTCTAGAGAAGGCTTCAAGGAAAGCTTAT AK021427 AK021427 25
    y TCTCATTCCAGCATGAGCGTTTCTGAGTCTCTTCAAGACGAATCTAGTTTTCACCTTCAC C15orf27 NM_152335 26
    y AGATCTTTGTAGGTTTAGACATGGCTCCCTGTCTCCAGTAAACATCCAGCCATTCAGACA PRDM4 NM_012406 27
    y AGTTCCAGATGTACATGGTATATTTTGAAGTAGAAATAAAAGAATTACTTATTTTTCTAA LOC165186 NM_199280 28
    CTCCATCTTATTTTCATGTATATGTGTTCATTAAAGCATGAATGGTATGGAACTCTCTCC IL2RA NM_000417 29
    y y AACCTGGAGCAATTTAAATAGGCTAAATGGTTTTGATTAAATCTTGAGCTCCGAGTTGGA ZNF697 NM_001080470 30
    y ACTGATGACTGCGCCTGTGTTCCAGAACTGTTCCGTCTCCCTGAGATCTATTCCCTCCAC CRYGA NM_014617 31
    y GAAATGTTCAGCAGATTTTGGTTTTGAATTTTCTTTCATCAGTATCACCCATATGAGCAG EEPD1 AF161370 32
    y y TCTAATTTTGAATTCTGACCATGGATACCCATCACTTTGGCATTCAGTGCTACATGTGTA LAMA3 NM_198129 33
    y CAATACCCATCTCGTGTATTAATCCCATCAATCATTCAGGTGTCTGGAATACAATTCTTT NEDD8 AK125214 34
    y y TGATCTTTCACTTGTTAACTAGGGAAAAACACTAGTCACCAGTGTGGTACAAACTTGTAC CA438802 CA438802 35
    y y TGTGTGGTAGAACTGAACAACGATAGACTGCTAACACATACTGTCTACAAAAATCTCAAT MCTP1 NM_024717 36
    y y AAGTCCAAGACTCAGTGATCGAAGGATGACAGAGATGTGCAGTGGGTATTGTTAGGAGAT HSD3B1 NM_000862 37
    y y ACATTACCTTCAGGAGACTTGATCCCAGTAGACTGAGGTCTTCCCTTTCAGCAGAAAGAT CYFIP2 NM_001037332 38
    y y TTGAGGTTGTCTGAGTCTTGGGTCTATGCCTTGAAAAAAGCTGAATTATTGGACAGTCTC IL2RB NM_000878 39
    CATTGTCAGTGCTACAGGAGTTACACCAAATGTAGAACCTTTTCTCCATGGTAACAGTTT PYROXD1 NM_024854 40
    y CAGAGGTGGGGCCATAGAATCCTACACTACAGCTTTCAGTTTTTTAGAAAATGTGATAAT XKR3 NM_175878 41
    y CAGCCTTTCCTCATGTCAACACAGTTCACAATATAGTTTTCAAAGTACAGTTTAAAACTC NT_035113.6 NT_035113.6 42
    y TGGGAGAGCGTTGGTGGATGTGTTCTGCATGTTCCTTTCTGTACAGTAACTTCTGCATTT THC2520461 THC2520461 43
    y TTGCTTTGAAAAGCTTCCTCCAAAAGCTGTATTGTGGTACTTTTGACTCTGGGACAAGAG THC2662025 THC2662025 44
    CACAGATGTTTTTCAAGTTCCTCAGTTTGTACTGAAATTAGGGATTCATCAGGGCAGGAA LL22NC03-5H6.5 NM_017931 45
    GTAATGCCTGGCCGCAGTGTGTGTGTATCCCATACCCCACTCTGGAAGGAACCATCCAGT POLR2L NM_021128 46
    CATTGTCAGTGCTACAGGAGTTACACCAAATGTAGAACCTTTTCTCCATGGTAACAGTTT PYROXD1 NM_024854 47
    AACAGTTAACAGGATGCAGACATGGCAGAGGTTTCCTAAAAATCTCATTATCTATAACCA MGC5370 BC006795 48
    CCAGGGTTGTAGCCCTGGATACTATCGGGATCATAAAGGCTTGTATACCGGACGGTGTGT LAMA3 NM_000227 49
    ATACATTTTAATTCCTCACGTTTTATATTGGAGAGTTCGGTACAGACTGTCCATTACTGC THC2650457 THC2650457 50
    TTTAAATCTCCACAGACGTATATGGATGGTTTACTGCATTATGTATCTGTAATAAGCGAC LAMA3 NM_198129 51
    TTCGTCACCTGTAGAGCGTTTGTCACTGTTCATCTGGTATTAAAGATTCCACATTCTCAT LOC645195 AK123450 52
    CCCCACAGGCCATGACCTTGAAGTGAAAGTCTTCTGTTGCTATTGTGGGCTCAAATATTT RNF141 NM_016422 53
    GTGAGTTCATGGAAGTCTAAATCAGTAATTTAGAGGATAGTGACACTCAATCAGTTTGTA RP4-692D3.1 AK024625 54
    TGCAGAGAGAATGTCTTCATAGAGAGAATGTCATTAAATACTTGAATCTGCATGACAGTT PSD3 NM_015310 55
    TAGATGAATGGATTATCTGCACTGATTGGGATGTCGGTTTTAGAGAGGGTCAACAGTATG ENST0000030 2942 ENST000003029 42 56
    ATCTTAGAAACACCTTGAAGTATGCCAAGAAAAACGTCCGTGCATTTTGGAAACTCAGAG APOL6 NM_030641 57
    AGATTACATTAATTTTTCTATAAATTGGAAGATTTATAAATGTTTGAAATTGTACACATT GK NM_203391 58
    CAGTGGAACTGATGGACACAAGCTTATCGCCACACTGGTTTTCCTCTGAAACAAGGCCCT MGC23270 BC015579 59
    CCTGGATAACCTGAGGCGAGTCATGCCATGCTACTCTAAAACCCAAAAACTTTCCAAGAT NEUROD4 NM_021191 60
    ATGTAACTGATTTTCTGCTAGAAGTTTGATATCCTCTGAATTTAGCTAAAGGATCACCAG SQSTM1 U46752 61
    CAAGTTTTCCTTGCTTTCCTGATACTCTTTGGCGCTGACTTGGAATTCTAAGAGCCTTGG RAD9A NM_004584 62
    CATATTCCATTTTTAAGAAGAGGTGTTCCAGTTCTGCATCTGATACCGTCTCCTTTCCCT QPCT NM_012413 63
    TGATCGAGAAGCTGCTCAATTATGCACCCCTGGAGAAGTGACCACGCTGAAACCCACCCA POLR2L NM_021128 64
    TTGAGGTTGTCTGAGTCTTGGGTCTATGCCTTGAAAAAAGCTGAATTATTGGACAGTCTC IL2RB NM_000878 65
    TTCTTGCCCTAAACAAGCAAAGAAAATGCAGAGGTCTCATCCTTAAGACTCAGAAGCTAA THC2677796 THC2677796 66
    CAGACTCTCCACATGTGCTCTACTAGTGAGTGCCTTATACTCTCAGTATTTTGGGGCTTA PPARA NM_005036 67
    CAGCCTTTCCTCATGTCAACACAGTTCACAATATAGTTTTCAAAGTACAGTTTAAAACTC NT_035113.6 NT_035113.6 68
    GCAATGAGTGAACTGACTGTGGCTACATTCTTGAAGATATACGGGAGAGACGTATTATTA CD521938 CD521938 69
    AACAGTTAACAGGATGCAGACATGGCAGAGGTTTCCTAAAAATCTCATTATCTATAACCA MGC5370 BC006795 70
    CCAAATTTATGTGGTTGTTACACTTCCATAGTTGTCTTAGCCGAATCCTTCCATATTCTT CCBL2 NM_019610 71
    TTCCAGATGAGCTCTTCTTTCCTACAAGTTTTCATAATTAGGGAATGCCAGGGTTTAGGG RNF41 NM_194358 72
    GTAATATGTGAAGATTAATGGCAATGAAGCAAACGTGCATAAGAAAATCCACGCAGCAAA LOC10013374 6 AK097452 73
    GCAAACTTGGCAGTCATAAACCCACATCTACTCTAACAAGTCTGAATGGTGCATAAGTAC WTAP NM_004906.3 74
    TTGGTTGTGAGATCCAGAATAACAGAAGCACTGGAGCATTCTGGAAGAATGCCTATGATG LOC646282 XR_017216 75
    CTTCTGTTAGCTCTGGACTCTTAACACTTAAGTTACTCTTCTGAAATTGCTAGGACCATT RBM4B NM_031492 76
    TGTACCTACTGATGGTGCTGTAACCACCTCACAGATTCCAGCTTCGGAACAAGAGACCCT MDM2 NM_006879 77
    TTTGATGTAGCTCTACCGATACTATGTGGTAATGCTATTTTGTTTTACTAACAAGCTCTG U68494 U68494 78
    CACTCCCTTGGAAAACAGTAAACATCATTTTGGAATGTGAACAACCAGAGACTACACAGG CTSC NM_148170 79
    ATCTTAGAAACACCTTGAAGTATGCCAAGAAAAACGTCCGTGCATTTTGGAAACTCAGAG APOL6 NM_030641 80
    TCCTGACAAGTTTTTCTCCCATGTCCGAGATGGCCTTAATTTTGGTACACAGATTGGCTT C13orf31 NM_153218 81
    AGTGACTCATTTACCAACATTAAACCCTAGGATAGATGCAACAGAGAAGTACTACTTCCT AK056973 AK056973 82
    TGAGCAGCTTGTGAATGTAACTGATGATCTACTCATATATAAGATCAGATTGGAAAAAGC TEKT1 NM_053285 83
    GTTCGAGAGCCGAGTCTGTGGGCACTCTCTGCCTTCATGCACCTGTCCTTTCTAACACGT CD81 NM_004356 84
    AAGCTGTGCCTCGACACATCCTCATCCCAAGCATGGGACACCTCAAGATGAATAATAATT ICOS NM_012092 85
    AATATTTGTGTAACGGAGATATACTACTGTAAGTTTTGTACTGTACTGGCTGAAAGTCTG IKZF4 NM_022465 86
    GCCTTTAGTTCTCCACTGGGGAGGAATCCTGGACCAAGCACAAAAACTTAACAAAAGTGA LAMB3 NM_001017402 87
    TTTGTGAAATAATGTACCATAGACTCTCACCAACTGTATATACCTGTACATATCAGAAGC DEPDC5 NM_014662 88
    AAGGTTCCATGGTAGCTAAGTGTGGACAAGCTAATCACTGAAGTTCCCTGATGCAGAGTT BC030122 BC030122 89
    TATGTACAGTTTACATGAATGTTCCTCAGGACATGGCATACAATGGCCTTGGAGGTCCAA APOL6 NM_030641 90
    TATTGTAAACTTTGTGGCTTTTGGTCTGTGATGCTTGGTCTCAAAGGAAAAAATAAGATG C8orf4 NM_020130 91
    ACATTAACCAGCTCCTGAGAACCATGTCTATGCCCAAAGGTAGAGTTCTGGATAAAAACC GPC3 NM_004484 92
    TGAACATGGAGGATGACCAGAACTGGTACAAGGCCGAGCTCCGGGGTGTCGAGGGATTTA GRAP NM_006613 93
    CAACACCATCCTCATCTGCATGGTGATCCTGCTGAACATCGGCCTGGCCATCCTCTTTGT JPH2 NM_020433 94
    GTGTGGAAACATCTATCCTATAGATCATCCTATTCTTATGTGTCTTTGGTTATCAGATCA QPCT NM_012413 95
    AGTTTCCTATGTTTCACTGTGCAAATATATCTGCTATTCTCCATACTCTGTAACAGTTGC CYP2C9 NM_000771 96
    GAAGGACAATGTCTGAATTAAATGCCGTGCTTTAAACTGAAAGGGAAACTTAGCAAATAA NT_026437.11 NT_026437.11 97
    ATACAAAGTGCAAAAAAGCTTGGCTCCTTCTGTATTCTTTAAAAACAAAACAACAACAAA CR622844 CR622844 98
    CAAGCTTCCTTCTTTCTAACCCCCAGACTTTGGCCTCTGAGTGAAATGTCTCTCTTTGCC PAX8 NM_003466 99
    AGACAATGGGAAAGTAAGTTATAAAAAATACTGGGAAATCTGTTTCTCTTCTGAGCAAGC C6orf105 NM_032744 100
    CGCAGCCTTCGGTATCCCCTGCACAGATAAGTTTGTCGTCTTTTCACAGATTGAGATATT IL3RA NM_002183 101
    AAATGCCATGCGGTTTTTCAACTTCTCATGGAGGGTCACTGCCGATCAGCTCAGGAAAGC ECE1 NM_001397 102
    AACAACGGGTTTCTGTTCCAACTGGTTGATCAACTTCTTGAGTCAACAAGTCCCAAAACC BC053669 BC053669 103
    GATGGATCCACTGGAGGTTAAGACATGTGGTAAGACAGTGTAATAGGAAGCTGCTCAGTT HLA-DMB BC035650 104
    GTGGGGAGGGTTTCTTGGGTTTCTTGAAGCCAGTATTTCCCATAGTATCTTACGTCCCAG C20orf200 NM_152757 105
    TAAACAGTAAAATAAGTACTCATCCGATAAATTCAAAGTAATTTTAGAACATTTTGACCA AF090895 AF090895 106
    ACAGCTCTAGAAATCCTTATGCCATTTGCAACTACATACCTTTGTGAGTTGGGATTTTCA LOC63920 NM_022090 107
    ACACTAAAAGTTGCTTCTAATAGGTGGCATATGTCTCTGCTGTGAATGACATGACCTTAC LOC642032 BC035659 108
    CTGATGGATGAGAAGTTTACATGCAATGATTTCTAGTAGCAGGTTCGTATAATTTTTCAC LOC400620 BC014643 109
    CGGCCTCCGCGGTGGACGTGTTCTTTTCTAAGCCATGGAGTGAGTGAGCAGGTGTGAAAT CHID1 NM_023947 110
    AGTTACAGAAGCCTGGGTAACTGCAGCTTCTTCACAGAGACTGGTTAGCAACCAGAGGCA VSTM3 NM_173799 111
    GCCAAAGGTTAAGACAATTGAACTTGAAGGAGGTCTTTTGGAAGATCACTTTGAAACTAC ERAP2 NM_022350 112
    GGTATTTTGAAGTACTGGGCTTATATTTAATTGGAATACATGTGTACAGCAATAAGCAGG PLEKHA5 NM_019012 113
    CTGAGCCCAAAACTCAAAGCCAAACCTGTCAGCTCTCTGAATGAGTGCACGACCAAGGAT SPTBN5 NM_016642 114
    AAAGCTTGGTGTTTTCTCTGGGTACACCCCAAGCAGCGTCTCCTTTTGGATACAGTTATT RHOH NM_004310 115
    ATCTTTATCTATGATGCTTTCAAGAAGATGATCAAGCTTGCAGATTACTACCCCATCAAC SLC4A4 NM_003759 116
    AGTCACAGTTACCGCGTGTACTACAATGCCGGCCCCAAGGATGAGGACCAGGACTACATC SCO2 NM_005138 117
    TGTGAGATGTTCCCCCTGCTGTAAATGCAGGTCTCTTGGTATTTATTGAGCTTTGTGGGA IER3 NM_003897 118
    AAACTCAAAGAGAAGGAGGGAGATCCGGTGTCCTTATTACATACAAGACTCAGGAACCCA CSF2RA NM_172249 119
    CCTAGCTGGACTCATGGTTCCTAAATAACCACGCTCAGAAGCTCTGCTAGGACTTACCCC FGD3 NM_033086 120
    TATTGTTAAGTTTCTGTTGACGGGTTAGAGAGCACGGGTTTGGCTGTGTGCTGGTTATTC THC2746246 THC2746246 121
    CAAAAGCAAGTCATGGCTAGAGTATCCATGCAAGGTGTCTTGTTGCATGGAAGGGATAGT TXNRD1 NM_003330 122
    GAGATGCCTGTGTAATTTCGTCCGAAGCTGCCAGGAAGAAGAACAGAACTTTGTGTGTTT IL3RA NM_002183 123
    AAAGAGGAATCGGGAAACCCTGGGTAAAAGTCGTCCAAGTGGAACTTCCTTTGGTCGGGG THC2515921 THC2515921 124
    AAAGGAAACGCGACGAAGAACTTGCCAAATCTATGGCCATATCCTTGTCTAAAATGTATA OTUD1 AB188491 125
    CAAAGATGCATTTACCTCTGTATCAACTCAGGAAATCTCATAAGCTGGTACCACTCAGGA GBP1 NM_002053 126
    CTGCCCCGGATGTGGCCGAGGGGCTTCACCCTGTGTCCTTAGGAGGGGGTGGCCTTGAGG BRF1 NM_145685 127
    GGCTGAACTACAAGTGTAGGCCACCATTATAATTTATAAATACAGCATACTTCAAAACTG RHOU NM_021205 128
    CCGTCTCTCTGCACAGCACAGAAATTCTCAATCACTGAAATGAGTAACTGCAAAATAAAT MPPE1 NM_023075 129
    GGTCTTGGTAGAAGCGCGTGCAAAAGCCATTCTGGACTTCCTGGATGCCCTGCTAGAGCT GSDML NM_001042471 130
    AGAACTGGAAGCTTGGAGGAAAGCATACTGGAGAATAAGCTACAAAGAGCCTGGGCTTAA CCDC142 NM_032779 131
    AGAAGTGGAACCGCTTACTACAGAAGGGATGGGTTGACTTTTTTGTTCCAAAGTTTTCCA SERPINA7 NM_000354 132
    GACTGTGGAATGGAATGACTCTCCAGAGCTGCAGATTGAAGGCATATTTTCATCTGACTT LOC387895 BC040060 133
    TGCTTTTGTCATAGTTCCACTCTCTCAGATACATGTATCTAATGAAACTGAATAAATCCG TAGAP NM_138810 134
    GACCCAGTCACACCATCCATGAAAAGCTGTTTCTATAATATGAAAAATTGTTAAATGACG AF143325 AF143325 135
    ATTACCCTATTTCACTGTTGTTCAAGTAAATCTAAACCTTGTAGACAAGTGAGTCATCTG PSD3 NM_015310 136
    TCACGCCCACACCAGATGATGCTGTGTTTCGCTGGCTCAGCACTGTCTATGCTGGCAGTA CPXM1 NM_019609 137
    ACCATGTGGAGATGTTTCTGGACTTGCTAGAGCCTGCTTAGCTGCATGTTTTGTAGTTAC LMAN2L NM_030805 138
    TGAAGACAGTCCCTATCCTAGAGGGGTTGAGCTTTCTTCCTCCTTGGGTTGGAGGAGACC SLC43A1 NM_003627 139
    TTGGAGAATGTGTAATTAGAGAACTATAAGATAAAGAGATAATCTTTAGAATTTGAATGT BC034791 BC034791 140
    GAAGACACTCCAGAAAATACAGAAACTGCATCTGTGTGCACCAAGGTCTGAAAAATGACT SLC23A1 NM_152685 141
    GGTCTTGGTAGAAGCGCGTGCAAAAGCCATTCTGGACTTCCTGGATGCCCTGCTAGAGCT GSDML NM_018530 142
    CAGCCTTTCCTCATGTCAACACAGTTCACAATATAGTTTTCAAAGTACAGTTTAAAACTC NT_035113 NT_035113 143
    TTTGTGTATCAAGTCCCACTATCAAGGATAAGCCAGTCCAGATTCGGCCTTGGAATCTCA CPEB4 NM_030627 144
    GAAGACACTCCAGAAAATACAGAAACTGCATCTGTGTGCACCAAGGTCTGAAAAATGACT SLC23A1 NM_152685 145
    AAGAACGAAAGAATAGTTAGGATACCAATGAGTAAAAGGGTTCCTGTTCACTCTGACTCT EFHD1 NM_025202 146
    GGCCATACGCCATGCCATAGCTTGTGCTATCTGTAAATATGAGACTTGTAAAGAACTGCC TAGAP NM_054114 147
    CTGCCCTGTGTTCGTGGTGCAGTGGCTGTTTGACGAGGCACAGCTGACGGTGGACAACGT NOTUM NM_178493 148
    GCTCAGGGAAGGGGCTGGGATCGGAACTTCCTGCTCTTGTTTCTGGACAACTTTCCCCTT KLHDC7B NM_138433 149
    CTTTAGACCTTTGTCCCCGTCACTGCCAGCGCTTGGGCTGAAGGAAGCTCCAGACTCAAT FXYD2 NM_021603 150
    CCCAGTGGAAAATCGCTTATATACCTATGACCACACAACCATCCTGGCCGTGGTGGCTGT HBEGF NM_001945 151
    TTTTGATGAGAATGAATCTTGGTACTTAGATGACAACATCAAAACATACTCTGATCACCC CP NM_000096 152
    GCAAAGCCTTCAAAATGTATCGTGCTTGAATTTTGACTCTTCTGAAATAGAATAACTGAC NUP50 NM_153645 153
    AGGATTTCAAGGAAGTGTTTGCTATTCAGGAAACAAATGGGAACAGTTGACTGGTTTAGT LOC93349 NM_138402 154
    CTTGGTTCATCTATTTTCATTAAACCATAGTCTTTGTCTGCTGGATGATACGTCGCCAAG THC2478115 THC2478115 155
    CCAAAACAGACATGAGCCCACTGCTTGGAACAACAAACTGTCCTGGTTGCTGGTCAGAGG HSD17B1 BC019592 156
    GGTCTTGGTAGAAGCGCGTGCAAAAGCCATTCTGGACTTCCTGGATGCCCTGCTAGAGCT GSDML NM_018530.2 157
    GGCAGCAGGAAGCGGAGTCGAGACCACTTCCGGAACAAGAGCAGCAGCCCCGAGGACCCA TSSC4 NM_005706 158
    CGGAAGTCCTGATGTATAGCAAGTTCAGCAGCAAATCTGACATTTGGGCTTTTGGGGTTT BTK NM_000061 159
    AGAACATTGTACCATGCCTCTTCTGTATCTGTGGAAGTTTCCTGTTTGACACAGGGTATC HMG2L1 NM_005487 160
    TCAGAAGGCTCTTCTGACTACTGGGCAAAGAGTGTAGATCAGAGCAGCAGTGAAAACAAT CXCR6 NM_006564 161
    ACTAGGAAGTATATGCCCCCAAATTATGAAATTCCATTTCAAACAGAATTAACAGAATTT ENST0000036 0738 ENST000003607 38 162
    TTTGGGGATTTTGTTTTCCCTTGGTCTAATGGAGAGAAAGACATTTTGGTTTTCTTTTTC MYT1 NM_004535 163
    GGTTTATTGACATGGAATGATTTGACCAAGGTGATATAGTGGTTAAGCAGTTAAGTGATT THC2699065 THC2699065 164
    CTGAGATGCTGATGTCATGGAGAGTAAACGACCACAAGTTTACCCCACTTCTCTGTGAAA NR1H4 NM_005123 165
    TCCAGATGTAAACCCCAAACTTGTACACAAAAGAAAGCACAGATTGTTTACCTGTTGTGG FHOD3 NM_025135 166
    CTTTAGACCTTTGTCCCCGTCACTGCCAGCGCTTGGGCTGAAGGAAGCTCCAGACTCAAT FXYD2 NM_021603 167
    GGGACATGGGAGGAGCCATATTGAGAAAGTAGCATGGGTACTTGGCTTCACAGAGTGTGG LOC729170 XM_001129548 168
    GCTGATTATTGGCATCATCTCCATTGTCCTACTCGGTTCTTAAAGGCATATGGACTTGCC LOC654433 AK126431 169
    AAGGTTCCATGGTAGCTAAGTGTGGACAAGCTAATCACTGAAGTTCCCTGATGCAGAGTT NT_006713.14 NT_006713.14 170
    ACAGCCCAGCAGGGAGGAAGCATCACACAGCGTTAGGAGCCGTTTCCTTCAGGTGTTAAG CHST10 NM_004854 171
    AGACATTGAGTCTTTTGGGAGACAGAAGGGAGGGAGAGTGCCAGTCAAAAGGGTTTCGTG BU953908 BU953908 172
    ATGAGCCGATGTTGACAAGAGCTTAAGTAAGTCTCCATGTACATCAAGTACTTTGGAGAC OFCC1 AF520801 173
    TGAAAAAGTGCACCACATGGATGTTAAGTAGAAATTCAAGAAAGTAAGATGTCTTCAGCA C8orf4 NM_020130 174
    GAGACAAACTCAATGTTAAAATCTCTAGGAGTGACCACGAAGTTTCATAGTTTTCCAAAT LYPLAL1 NM_138794 175
    GATCAGCACCTATGAGTTCGGCAAAAGCTTCTTCCAGAGGCTGAACCAGGACCGGCTTCT SLC25A39 NM_016016 176
    TTTAAATCTCCACAGACGTATATGGATGGTTTACTGCATTATGTATCTGTAATAAGCGAC LAMA3 NM_198129 177
    GGAAGGCTTCTGACGCTTGTGGCCAGACTGCAATTGCACTTATGTGTTATGCTACTAATA ZDHHC14 NM_153746 178
    AGAAACCAGGAACTATGTTAAACAAAGAAAAGCTTTTGGCAAAACAGTTGCTCACCTACA ACADL NM_001608 179
    AAAGATGGTGGCTGTGTCTCTCCCCGGTAATGTCACTGTTTTTATTCCTTCCATCTAGCA CASC3 NM_007359 180
    CTATAAGGTTGTACTGCTGGGAAAATACAATGCACAGGGCTTAGGTTCAGATCATGAATT PYROXD1 NM_024854 181
    TCAATGTAAAAACTAGAACCTTTATATACTGGGGATTATAAGATTCTACTTACTAGAAAT LCORL AL133031 182
    GATCCCTTCTCAAACTCAGAACCCTAGCAGTGTTACCTTAAACAAAAATGAGCTCGAGAA MGC12966 NM_001037163 183
    AACGCTGTCCGCATCATCCAGGTCTATTGGCGCTGGAGAAGTTGCCATACCCGTGGCTTT THC2623157 THC2623157 184
    TGGGGACAGCCAAGTTTTGTTGATAAACCTATTTCCTAGCATGCCTTCAGGAAGTTGTGC BTBD11 NM_001018072 185
    TCACTCAGGACTTCTCTCCTGAAGAACACGCAGTGCTAAAACTGAGGATGATTTCCCTAA PTPN7 NM_080588 186
    GAACTGAACATTGTTTGTAAGGCTGTGGATGATGGTTACAATGTGCAGCCAGACACCGTG SUOX NM_000456 187
    GGTCTTGGTAGAAGCGCGTGCAAAAGCCATTCTGGACTTCCTGGATGCCCTGCTAGAGCT GSDML NM_018530 188
    GAAACAAGTGCCATGAGGCCCTCAAGCCAAACTCTTCCAACTGAATAAATGAGCTAATTC THC2727170 THC2727170 189
    TCACCCTGCATATCCTAGGTTTGAAGAGAAACGCTCAGATCCGCTTATTTCTGCCAGTAT RNH1 NM_203389 190
    TGAGCCAAGCACAGTGGTGGCAAAAGCTTATTTGTGTACAATCACTGGCTTCATACTTCC RPP40 NM_006638 191
    TGTGTGCATAGTTACTCAGTTTTTATGAACTGTTGTATCCTGTTAATGCATATTGCTCTG WTAP NM_004906 192
    TGGCACACCGTCAACAACACGATCCCTATGTCCATGTGTTCCAAGAGGTGCCAGTCAGGG TAS1R2 NM_152232 193
    TATGTACAGTTTACATGAATGTTCCTCAGGACATGGCATACAATGGCCTTGGAGGTCCAA APOL6 NM_030641 194
    AAATAGCATGTGACACAGGACAGCCATAGTATAGTGTGTCACTCGTGGTTGGTGTCCTTT TNFRSF10B NM_003842 195
    AGTGCTGGCCCAGAACAGGTTTCTCCTGGAGCTACAGATAAGCAACAACAGGCTGGAGGA RNH1 NM_002939 196
    TGTCCTTCATTCTTTTGATGTGATGTATCGCATTTACAGATCTGAATATGTATTAGGTGG AF119879 AF119879 197
    TGACTGTTTTAATGGGGTTTCACCCAAATTGTTTAATGCTTCTGCTGTAAATGTCATACT INSM2 NM_032594 198
    TGACTATGAGACCGTTCGCAATGGGGGCCTGATCTTCGCTGGACTGGCCTTCATCGTGGG FXYD2 NM_021603 199
    AATCCCATGGACCCTCTGGACTACAAGGATCAGAGTGCCTGGAAGTTTCAGATCTTGTAG CRX NM_000554 200
    ATGGGTAATATCAGCATAATTGTATTGATCAGAAGAAGTCATCATCTTCATACACCCATG OR5P3 NM_153445 201
    TGGAATAATGTTCTCTGCTACTTTTAACCTGATTTTCTTTGTACCTAAATAGGCAGCTAG SIRT5 NM_031244 202
    ACAATAAGTTCTGCAAAACCCTCTCATTCATGAAAAGGTGCTCCTTGCTAGACAGAAACT ARID2 NM_152641 203
    ACACGTTTTTGGAGGATACCAAGAAGCTGTACCACTCAGAAGCCTCTTCCATCAACTTCA SERPINA1 NM_000295 204
    GGAAGGCTTCTGACGCTTGTGGCCAGACTGCAATTGCACTTATGTGTTATGCTACTAATA ZDHHC14 NM_153746.1 205
    GCTCTTAGAACCTCAGGTTCTCAGGCAAGAGCCACCTGCTATTGCCGAACTGGCCGTTGT DEFA5 NM_021010 206
    GCAGGATAAGGACAAGGCTACACAATGGCTTAGAACAGTTAATCGGGCAACAGTTGGAAA THC2505770 THC2505770 207
    CGCATAATTCGGCTCATCTCCTTAGCTGCCCAGAAATTCATCTCAGATATTGCCAATGAT TAF10 NM_006284 208
    TAACGTTTCCGGTATTACTCTGCTACACGTAGCCTTTTTACTTTTGGGGTTTTGTTTTTG CD81 NM_004356 209

Claims (16)

  1. A method for typing a RNA sample of an individual suffering from colorectal cancer or suspected of suffering therefrom, the method comprising
    a. providing an RNA sample that is prepared from a tissue sample from said individual, said tissue sample comprising colorectal cancer cells or suspected to comprise colorectal cancer cells;
    b. determining RNA levels for a set of genes in said RNA sample;
    and
    c. typing said RNA sample on the basis of the RNA levels determined for said set of genes;
    wherein said set of genes comprises at least two of the genes listed in Table 1.
  2. The method of claim 1, wherein said set of genes comprises at least ten of the genes listed in Table 1.
  3. The method of claim 1, whereby said set of genes comprises MCTP1, LAMA3, CTSC, PYROXD1, EDEM1, IL2RB, ZNF697, SLC6A12, IL2RA, CYXIP2, PIM3, LIF, M6PRBP1, CA438802, HSD3B1, ZBED4, PPARA, THNSL2.
  4. The method according to any of claims 1-3, whereby said RNA levels are determined by microarray analysis.
  5. The method according to any of the previous claims, further comprising normalizing the determined RNA levels of said set of genes in said sample.
  6. The method according to any of the previous claims, whereby said colorectal cancer comprises a TNM stage II or TNM stage III cancer according to the TNM Staging System.
  7. The method according to any of the previous claims, whereby said typing differentiates cancer cells with a low metastasizing potential and cancer cells with a high metastatic potential.
  8. A method of classifying an individual suffering from colorectal cancer, comprising:
    classifying said individual as having a poor prognosis or a good prognosis by a method comprising:
    (a) providing an RNA sample from a said individual that is prepared from a tissue sample from said individual, said tissue sample comprising colorectal cancer cells or suspected to comprise colorectal cancer cells;
    (b) determining a level of RNA for a set of genes comprising at least two of the genes listed in Table 1 in said sample;
    (c) determining a similarity value between a level of expression from the set of genes in said individual and a level of expression from said set of genes in a patient having no recurrent disease within five years of initial diagnosis; and
    (d) classifying said individual as having a poor prognosis if said similarity value is below a first similarity threshold value, and classifying said individual as having a good prognosis if said similarity value exceeds said first similarity threshold value.
  9. The method of claim 8, whereby the determined level of RNA for said set of genes is normalized.
  10. A method of assigning treatment to a individual suffering from colorectal cancer, comprising
    (a) classifying said individual as having a good prognosis or a poor prognosis according to claim 8 or claim 9;
    (b) assigning chemotherapy if said individual is classified as having said poor prognosis.
  11. The method according to any of the previous claims, whereby said colorectal cancer comprises a colon cancer.
  12. A method of developing a colorectal gene signature for typing a RNA sample of an individual suffering from colorectal cancer or suspected of suffering therefrom, comprising determining a set of genes associated with a distant metastasis free survival period in RNA samples obtained from non-MSI colorectal cancers.
  13. A method of developing a colorectal gene signature for typing an RNA sample of an individual suffering from colorectal cancer or suspected of suffering therefrom, comprising determining a set of genes associated with a distant metastasis free survival period in RNA samples obtained from colorectal cancer samples having a valine at position 600 of B-Raf.
  14. A nucleotide microarray, comprising a total of between 100 and 12.000 nucleic acid molecules, at least two of said nucleic acid molecules being able to hybridize to a set of genes comprising at least two of the genes listed in Table 1.
  15. The microarray of claim 14, further comprising at least five nucleic acid molecules being able to hybridize to a set of genes comprising at least five of the genes listed in Table 2.
  16. The use of an array according to claim 14 or claim 15 to differentiate colorectal cancer cells with a low versus a high metastasizing potential.
EP08172911A 2008-12-24 2008-12-24 Methods and means for typing a sample comprising colorectal cancer cells Withdrawn EP2202320A1 (en)

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EP08172911A EP2202320A1 (en) 2008-12-24 2008-12-24 Methods and means for typing a sample comprising colorectal cancer cells
EP09775361A EP2379740A1 (en) 2008-12-24 2009-12-23 Methods and means for typing a sample comprising colorectal cancer cells.
NZ593847A NZ593847A (en) 2008-12-24 2009-12-23 Methods and means for typing a sample comprising colorectal cancer cells
AU2009330807A AU2009330807B2 (en) 2008-12-24 2009-12-23 Methods and means for typing a sample comprising colorectal cancer cells.
MX2011006926A MX2011006926A (en) 2008-12-24 2009-12-23 Methods and means for typing a sample comprising colorectal cancer cells.
PCT/NL2009/050797 WO2010074573A1 (en) 2008-12-24 2009-12-23 Methods and means for typing a sample comprising colorectal cancer cells.
CN200980157369.0A CN102325902B (en) 2008-12-24 2009-12-23 The sample comprising colorectal cancer cell is carried out to the method and apparatus of somatotype
JP2011543452A JP2012513752A (en) 2008-12-24 2009-12-23 Methods and means for typing samples containing colorectal cancer cells
US13/141,742 US8921051B2 (en) 2008-12-24 2009-12-23 Methods and means for typing a sample comprising colorectal cancer cells
CA2748224A CA2748224A1 (en) 2008-12-24 2009-12-23 Methods and means for typing a sample comprising colorectal cancer cells

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WO2012087144A3 (en) * 2010-12-23 2012-09-20 Agendia N.V. Methods and means for molecular classification of colorectal cancers
WO2012044167A3 (en) * 2010-09-28 2013-08-01 Agendia N.V. Methods and means for typing a sample comprising cancer cells based on oncogenic signal transduction pathways
CN113774130A (en) * 2020-06-09 2021-12-10 碳逻辑生物科技(香港)有限公司 Biomarkers and methods for selecting a group of chemotherapy responsive patients and uses thereof

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JP7024957B2 (en) * 2017-07-04 2022-02-24 株式会社Ｄｎａチップ研究所 Methods for predicting the presence or absence of metastatic metastasis of colorectal cancer and kits used for it
CN109988708B (en) * 2019-02-01 2022-12-09 碳逻辑生物科技(中山)有限公司 System for typing a patient suffering from colorectal cancer
CN111798927A (en) * 2020-07-10 2020-10-20 武汉大学 Construction method of first-choice molecular typing of group ketogenic diet clinical research patients

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